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yangrc3 luisviolinist braveheart3118 zcy1062000 duosu shenglei1988 rnaimehaom mengzhiyaa jing-xinxing linuxpham mvfki dhtc kaliberaleidenbase's Issues
Cannot install leidenbase due to compilation issue
When attempting to install leidenbase on R 3.6.2 and MacOS 10.15.2, I keep getting the following error during compilation:
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Here is my install.out file.
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.2
Install leidenbase failed
Hi,
When I install leidenbase using Rstudio (R 4.0.5) and as following codes devtools::install_github('cole-trapnell-lab/leidenbase') ,
an error occured:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [leidenbase.so] Error 1
ERROR: compilation failed for package ‘leidenbase’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/leidenbase’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/db/2pdswwk10pxdhvxh0854wtdr0000gn/T//RtmpfFyzEF/file62966a038d47/leidenbase_0.1.3.tar.gz’ had non-zero exit status
my PC is macOS 11, and cpu is M1. Before install leidenbase, the gfortran 11 is download and install successfully from wedsite: https://github.com/fxcoudert/gfortran-for-macOS/releases
what can i do for this problem?
I appreciate your solicitude, expect that is your to reply!
Tag a release?
Now that monocle 3 has a release requiring this, could you tag a release? We can then package this in bioconda.
Can't install leidenbase package
Hello,
After some time of unsuccessful troubleshooting, I keep getting this error when I try to install it.
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘leidenbase’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so, 6): Library not loaded: @rpath/libxml2.2.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
- removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘/var/folders/6n/fybw2ts966dc3jhc1gqw8hxh90fnjj/T//Rtmp7KxBMu/file9c11f034b50/leidenbase_0.1.0.tar.gz’ had non-zero exit status
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 ps_1.3.0 prettyunits_1.0.2 rprojroot_1.3-2
[5] digest_0.6.21 crayon_1.3.4 withr_2.1.2 assertthat_0.2.1
[9] R6_2.4.0 backports_1.1.4 magrittr_1.5 rlang_0.4.0
[13] cli_1.1.0 curl_4.2 fs_1.3.1 remotes_2.1.0
[17] testthat_2.2.1 callr_3.3.2 ellipsis_0.3.0 desc_1.2.0
[21] devtools_2.2.1 tools_3.6.1 glue_1.3.1 pkgload_1.0.2
[25] compiler_3.6.1 processx_3.4.1 pkgbuild_1.0.5 sessioninfo_1.1.1
[29] memoise_1.1.0 usethis_1.5.1
Can someone please help me?
thanks in advance.
Sync with upstream C++ base
Hi all-figured I'd let you know that there is now a c++ maintained version of leidenalg that just cut a release.
https://github.com/vtraag/libleidenalg/releases/tag/0.10.0
Likely easier to maintain.
Unable to install leidenbase on Mac OSX Big Slur 11.1
Hi,
I tried multiple ways (e.g. updating gfortran to 10.2, the specific package for Intel Mac Big Sur), but all the ways did not work, and the installation still gives error message:
devtools::install_github('cole-trapnell-lab/leidenbase')
Downloading GitHub repo cole-trapnell-lab/leidenbase@HEAD
✓ checking for file ‘/private/var/folders/_l/5nz8_9gj36jgw7_xx72nxl7c0000gq/T/RtmpFB0FRX/remotes29d83e33752d/cole-trapnell-lab-leidenbase-8c52ebc/DESCRIPTION’ ...
─ preparing ‘leidenbase’: (348ms)
✓ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories (596ms)
─ building ‘leidenbase_0.1.2.tar.gz’
- installing source package ‘leidenbase’ ...
** using staged installation
checking for gcc... /usr/local/opt/llvm/bin/clang
checking whether the C compiler works... no
configure: error: in/private/var/folders/_l/5nz8_9gj36jgw7_xx72nxl7c0000gq/T/RtmpLK8xEs/R.INSTALL2be3207c3b6b/leidenbase': configure: error: C compiler cannot create executables Seeconfig.log' for more details
ERROR: configuration failed for package ‘leidenbase’ - removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘/var/folders/_l/5nz8_9gj36jgw7_xx72nxl7c0000gq/T//RtmpFB0FRX/file29d82ca0aaf/leidenbase_0.1.2.tar.gz’ had non-zero exit status
My system versions:
1. On R:
version
_
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 0.3
year 2020
month 10
day 10
svn rev 79318
language R
version.string R version 4.0.3 (2020-10-10)
nickname Bunny-Wunnies Freak Out
2. gfortran:
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin20/10.2.0/lto-wrapper
Target: x86_64-apple-darwin20
Configured with: ../gcc-10.2.0/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/build_package/deps --with-isl=/Users/fx/devel/gcc/build_package/deps --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin20 --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 10.2.0 (GCC)
Please help me with this, thank you so much!
This issue applies to both lmidenbase and monocle3 but was originally posted in the monocle3 repository.
I am also having this problem resulting in the exact same error message (see below). Nothing I have tried has worked, either. The computer I'm using is a macOS Catalina, Version 10.15.6. I'm new to GitHub so please let me know if you need more information! Thanks!
In file included from cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c:63:
In file included from cigraph/src/igraph_blas_internal.h:33:
cigraph/src/config.h:131:9: warning: 'PACKAGE_VERSION' macro redefined [-Wmacro-redefined]
#define PACKAGE_VERSION "1.1.0"
^
:7:9: note: previous definition is here
#define PACKAGE_VERSION "0.8.2"
^
In file included from cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c:80:
cigraph/src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c:510:17: error: implicit declaration of function 'dsyrk_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
BLAS_dsyrk ("L", "N",
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:331:2: note: expanded from macro 'BLAS_dsyrk'
BLAS_DSYRK (uplo, trans, &N, &K, alpha, A, &LDA, beta, C, &LDC) ;
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:132:20: note: expanded from macro 'BLAS_DSYRK'
#define BLAS_DSYRK igraphdsyrk_
^
cigraph/src/igraph_lapack_internal.h:86:29: note: expanded from macro 'igraphdsyrk_'
#define igraphdsyrk_ dsyrk_
^
In file included from cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c:80:
cigraph/src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c:713:13: error: implicit declaration of function 'dpotrf_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
LAPACK_dpotrf ("L",
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:365:2: note: expanded from macro 'LAPACK_dpotrf'
LAPACK_DPOTRF (uplo, &N, A, &LDA, &INFO) ;
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:135:23: note: expanded from macro 'LAPACK_DPOTRF'
#define LAPACK_DPOTRF igraphdpotrf_
^
cigraph/src/igraph_lapack_internal.h:120:29: note: expanded from macro 'igraphdpotrf_'
#define igraphdpotrf_ dpotrf_
^
cigraph/src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c:713:13: note: did you mean 'zpotrf_'?
cigraph/src/CHOLMOD/Include/cholmod_blas.h:365:2: note: expanded from macro 'LAPACK_dpotrf'
LAPACK_DPOTRF (uplo, &N, A, &LDA, &INFO) ;
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:135:23: note: expanded from macro 'LAPACK_DPOTRF'
#define LAPACK_DPOTRF igraphdpotrf_
^
cigraph/src/igraph_lapack_internal.h:120:29: note: expanded from macro 'igraphdpotrf_'
#define igraphdpotrf_ dpotrf_
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:370:6: note: 'zpotrf_' declared here
void LAPACK_ZPOTRF (char *uplo, BLAS_INT *n, double *A, BLAS_INT *lda,
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:144:23: note: expanded from macro 'LAPACK_ZPOTRF'
#define LAPACK_ZPOTRF zpotrf_
^
In file included from cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c:80:
cigraph/src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c:842:17: error: implicit declaration of function 'dtrsm_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
BLAS_dtrsm ("R", "L", "C", "N",
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:257:2: note: expanded from macro 'BLAS_dtrsm'
BLAS_DTRSM (side, uplo, transa, diag, &M, &N, alpha, A, &LDA, B, &LDB);
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:130:20: note: expanded from macro 'BLAS_DTRSM'
#define BLAS_DTRSM igraphdtrsm_
^
cigraph/src/igraph_blas_internal.h:50:29: note: expanded from macro 'igraphdtrsm_'
#define igraphdtrsm_ dtrsm_
^
cigraph/src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c:842:17: note: did you mean 'ztrsm_'?
cigraph/src/CHOLMOD/Include/cholmod_blas.h:257:2: note: expanded from macro 'BLAS_dtrsm'
BLAS_DTRSM (side, uplo, transa, diag, &M, &N, alpha, A, &LDA, B, &LDB);
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:130:20: note: expanded from macro 'BLAS_DTRSM'
#define BLAS_DTRSM igraphdtrsm_
^
cigraph/src/igraph_blas_internal.h:50:29: note: expanded from macro 'igraphdtrsm_'
#define igraphdtrsm_ dtrsm_
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:261:6: note: 'ztrsm_' declared here
void BLAS_ZTRSM (char *side, char *uplo, char *transa, char *diag, BLAS_INT *m,
^
cigraph/src/CHOLMOD/Include/cholmod_blas.h:139:20: note: expanded from macro 'BLAS_ZTRSM'
#define BLAS_ZTRSM ztrsm_
^
In file included from cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c:80:
cigraph/src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c:141:40: warning: unused variable 'tstart' [-Wunused-variable]
double one [2], zero [2], fjk [2], tstart ;
^
2 warnings and 3 errors generated.
make: *** [cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
- removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘/var/folders/v3/tdmhdpxd65n0j81wk859jdsw0000gq/T//Rtmph6G87V/file13db743faeb27/leidenbase_0.1.1.tar.gz’ had non-zero exit status
Originally posted by @val23n in cole-trapnell-lab/monocle3#393 (comment)
Mac OS monterey clang: error: linker command failed with exit code 1
I met all the requirements
MacOS Monterey on Apple ARM CPU
R distribution: https://cran.r-project.org/bin/macosx/big-sur-arm64/base/R-4.1.2-arm64.pkg C/C++ compilers: Xcode 13.2.1 FORTRAN compiler: gfortran 11.0 https://mac.r-project.org/libs-arm64/gfortran-f51f1da0-darwin20.0-arm64.tar.gz Note: after downloading gfortran, use the command sudo tar fxz gfortran-f51f1da0-darwin20.0-arm64.tar.gz -C / to install it to /opt. For more information, see https://mac.r-project.org/tools/
especially with gfortran, i have deleted my previous one and re-installed.
However I am having such error when installing leidenbase.
Any ideas about it?
Thank you!
Failed to use leidenbase::leiden_find_partition
Hello:
When I used the function, I got an error like:
leidenbase::leiden_find_partition
Error: read failed on ~/R/x86_64-pc-linux-gnu-library/4.2/leidenbase/R/leidenbase.rdb
In addition: Warning message:
restarting interrupted promise evaluation
Can the author help me?
installation failure on R
Hello,
I have faced the failure of installation on my system. Here is my system info.
Mac: Big Sur 11.2.2
R: version 4.1.0
RStudio: version 1.4.1717
gcc: Apple clang version 11.0.3 (clang-1103.0.32.62)
Here is error messages I got:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [leidenbase.so] Error 1
ERROR: compilation failed for package ‘leidenbase’
- removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/leidenbase’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/fb/63zhxstn6bvc52qb8hgjc1c40000gn/T//RtmpFIGzE4/filedad63dbdc040/leidenbase_0.1.3.tar.gz’ had non-zero exit status
Is still gcc is the cause of error? Or if you have any further advises, feel free to let me know. Thanks in advance!
Installation fails likely due to gcc/fortran new argument type enforcement
Hi,
installing the leidenbase package via devtools::install_github('cole-trapnell-lab/leidenbase') fails with the following error message:
arpack/dgetv0.f:404:38:
367 | call igraphdvout (logfil, 1, rnorm0, ndigit,
| 2
......
404 | call igraphdvout (logfil, n, resid, ndigit,
| 1
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
It seems to be similar to this issue: scipy/scipy#11611
My gcc/g++/gfortran version is 10.1.0.
sessionInfo():
R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] rstudioapi_0.11 magrittr_1.5 usethis_1.6.1 devtools_2.3.0 pkgload_1.1.0 R6_2.4.1 rlang_0.4.6
[8] fansi_0.4.1 tools_4.0.1 pkgbuild_1.0.8 sessioninfo_1.1.1 cli_2.0.2 withr_2.2.0 ellipsis_0.3.1
[15] remotes_2.1.1 assertthat_0.2.1 digest_0.6.25 rprojroot_1.3-2 crayon_1.3.4 processx_3.4.2 callr_3.4.3
[22] fs_1.4.2 ps_1.3.3 curl_4.3 testthat_2.3.2 memoise_1.1.0 glue_1.4.1 compiler_4.0.1
[29] desc_1.2.0 backports_1.1.8 prettyunits_1.1.1 renv_0.11.0
Makeconf
CC = gcc
CFLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -D_FORTIFY_SOURCE=2
CXX = g++ -std=gnu++11
## Not used by anything in R, in particular not for the .cc.d rule
## but used via R CMD config by several packages
CXXCPP = $(CXX) -E
CXXFLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt $(LTO)
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt $(LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = g++
CXX14FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt $(LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = g++
CXX17FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt $(LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX20 = g++
CXX20FLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt $(LTO)
CXX20PICFLAGS = -fpic
CXX20STD = -std=gnu++20
CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
F_VISIBILITY = -fvisibility=hidden
## FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran
FCFLAGS = -g -O2 $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -g -O2 $(LTO)
FLIBS = -lgfortran -lm -lquadmath
Issue installing leidenbase on Mac OSX (10.14.6)
Hi,
I am encountering issues installing leidenbase on a Mac OSX (10.14.6).
The error message is as follows:
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'leidenbase' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-leidenbase-0.1.0/00new/leidenbase/libs/leidenbase.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-leidenbase-0.1.0/00new/leidenbase/libs/leidenbase.so, 6): Library not loaded: @rpath/libgfortran.3.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-leidenbase-0.1.0/00new/leidenbase/libs/leidenbase.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/leidenbase'
I checked @rpath, and did not find libgfortran.3.dylib, but libgfortran.5.dylib instead:
$ ll /Library/Frameworks/R.framework/Libraries/
total 19208
-rwxrwxr-x 1 root admin 3.9M Mar 31 19:41 libR.dylib
drwxrwxr-x 3 root admin 96B Apr 24 2020 libR.dylib.dSYM
-rwxrwxr-x 1 root admin 221K Mar 31 19:41 libRblas.dylib
drwxrwxr-x 3 root admin 96B Apr 24 2020 libRblas.dylib.dSYM
-rwxrwxr-x 1 root admin 2.1M Mar 31 19:41 libRlapack.dylib
drwxrwxr-x 3 root admin 96B Apr 24 2020 libRlapack.dylib.dSYM
-rw-rw-r-- 1 root admin 157K Mar 31 19:41 libgcc_s.1.dylib
-rwxrwxr-x 1 root admin 2.7M Mar 31 19:41 libgfortran.5.dylib
-rwxrwxr-x 1 root admin 302K Mar 31 19:41 libquadmath.0.dylib
R sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.5
I have included the full output from the installation in a (gzipped) text file.
Please let me know if I can provide additional information.
Thank you.
Unable to install leidenbase
Hi,
I am trying to install monocle3 on RStudio and have to install leidenbase. I executed the command 'devtools::install_github('cole-trapnell-lab/leidenbase')', but get an error:
.
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘leidenbase’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/bst/Library/R/4.0/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so':
dlopen(/Users/bst/Library/R/4.0/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so, 6): Symbol not found: ___addtf3
Referenced from: /usr/local/lib/libquadmath.0.dylib
Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
in /usr/local/lib/libquadmath.0.dylib
Error: loading failed
Execution halted
ERROR: loading failed
- removing ‘/Users/bst/Library/R/4.0/library/leidenbase’
=========== Details on gcc, gfortran ====
| => gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin19.6.0
| => gfortran --version
GNU Fortran (Homebrew GCC 10.2.0_4) 10.2.0
======================
My RStudio 'Makeconf' file shows:
AR = ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY =
CC = clang -mmacosx-version-min=10.13
CFLAGS = -Wall -g -O2 $(LTO)
CPICFLAGS = -fPIC
CPPFLAGS = -I/usr/local/include
CXX = clang++ -mmacosx-version-min=10.13 -std=gnu++11
Not used by anything in R, in particular not for the .cc.d rule
but used via R CMD config by several packages
CXXCPP = $(CXX) -E
CXXFLAGS = -Wall -g -O2 $(LTO)
CXXPICFLAGS = -fPIC
CXX11 = clang++ -mmacosx-version-min=10.13
CXX11FLAGS = -Wall -g -O2 $(LTO)
CXX11PICFLAGS = -fPIC
CXX11STD = -std=gnu++11
CXX14 = clang++ -mmacosx-version-min=10.13
CXX14FLAGS = -Wall -g -O2 $(LTO)
CXX14PICFLAGS = -fPIC
CXX14STD = -std=gnu++14
CXX17 = clang++ -mmacosx-version-min=10.13
CXX17FLAGS = -Wall -g -O2 $(LTO)
CXX17PICFLAGS = -fPIC
CXX17STD = -std=gnu++17
CXX20 = clang++ -mmacosx-version-min=10.13
CXX20FLAGS = -Wall -g -O2 $(LTO)
CXX20PICFLAGS = -fPIC
CXX20STD = -std=gnu++2a
CXX_VISIBILITY =
DYLIB_EXT = .dylib
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress#
should be used by packges for dylibs, but at the time of writing was not
DYLIB_LINK =
ECHO = echo
ECHO_C = \c
ECHO_N =
ECHO_T =
F_VISIBILITY =
FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran -mmacosx-version-min=10.13
FCFLAGS = -Wall -g -O2 $(LTO_FC)
additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -Wall -g -O2 $(LTO_FC)
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
FPICFLAGS = -fPIC
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS = -framework Foundation
JAR = /usr/bin/jar
==============
My R sessionInfo() is:
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 magrittr_2.0.1 usethis_2.0.1 devtools_2.3.2 pkgload_1.1.0
[6] R6_2.5.0 rlang_0.4.10 fastmap_1.1.0 tools_4.0.3 pkgbuild_1.2.0
[11] sessioninfo_1.1.1 cli_2.3.0 withr_2.4.1 ellipsis_0.3.1 remotes_2.2.0
[16] assertthat_0.2.1 rprojroot_2.0.2 lifecycle_1.0.0 crayon_1.4.1 processx_3.4.5
[21] purrr_0.3.4 callr_3.5.1 fs_1.5.0 ps_1.5.0 curl_4.3
[26] testthat_3.0.2 memoise_2.0.0 glue_1.4.2 cachem_1.0.4 compiler_4.0.3
[31] desc_1.2.0 prettyunits_1.1.1bst
What do I need to do? Thanks for your help!
"Failure (test-leidenbase.R:253:5): modularity and significance return values" for architectures arm64, i386, ppc64el and s390x
Hi,
the Debian packaged version of leidenbase has to pass its test on different architectures. This works well for amd64 and others. However, for some architectures there is a failure. You might like to look at the full log of the CI test for arm64. It contains this snippet which seems to be relevant:
BEGIN TEST testthat.R
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> testthat::test_check("leidenbase")
Loading required package: leidenbase
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-leidenbase.R:253:5): modularity and significance return values ──
`t11_v01` not equal to `t11_v01_expect`.
1/1 mismatches
[1] 0.71 - 0.71 == 0.000133
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
Error: Test failures
Execution halted
This error occurs for the architectures arm64, i386, ppc64el and s390x.
For i386 there are even more errors ( here you can find the log ) but may be I should open a different issue once the issue above is fixed.
Kind regards, Andreas.
leidenbase compilation failed Mac OS X
Hello, I am getting the following error when I try to install leidenbase:
ld: file not found: /usr/lib/system/libsystem_symptoms.dylib for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [leidenbase.so] Error 1
ERROR: compilation failed for package ‘leidenbase’
- removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’
I was wondering if you have any advice?
Cannot install leidenbase in anaconda environment
I do not manage to install leidenbase, it would be great if I could get some help!
Computer System: openSUSE Leap 15.1
compilers:
(spols200116) crick> cc --version
cc (SUSE Linux) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
(spols200116) crick> gcc --version
gcc (SUSE Linux) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
(spols200116) crick> clang --version
If 'clang' is not a typo you can use command-not-found to lookup the package that contains it, like this:
cnf clang
(spols200116) crick> c++ --version
c++ (SUSE Linux) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
(spols200116) crick> g++ --version
g++ (SUSE Linux) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
(spols200116) crick> clang++ --version
If 'clang++' is not a typo you can use command-not-found to lookup the package that contains it, like this:
cnf clang++
(spols200116) crick> f77 --version
If 'f77' is not a typo you can use command-not-found to lookup the package that contains it, like this:
cnf f77
(spols200116) crick> f95 --version
If 'f95' is not a typo you can use command-not-found to lookup the package that contains it, like this:
cnf f95
(spols200116) crick> gfortran --version
GNU Fortran (SUSE Linux) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
(spols200116) crick> flang --version
If 'flang' is not a typo you can use command-not-found to lookup the package that contains it, like this:
cnf flangR 3.6.1 was installed with Anaconda
Makeconf:
# etc/Makeconf. Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
#
# R was configured using the following call
# (not including env. vars and site configuration)
# configure '--prefix=/home/fabrost/miniconda3/envs/spols200116' '--host=x86_64-conda_cos6-linux-gnu' '--build=x86_64-conda_cos6-linux-gnu' '--enable-shared' '--enable-R-shlib' '--with-blas=-lblas' '--with-lapack=-llapack' '--disable-prebuilt-html' '--enable-memory-profiling' '--with-tk-config=/home/fabrost/miniconda3/envs/spols200116/lib/tkConfig.sh' '--with-tcl-config=/home/fabrost/miniconda3/envs/spols200116/lib/tclConfig.sh' '--with-x' '--with-pic' '--with-cairo' '--with-readline' '--with-recommended-packages=no' '--without-libintl-prefix' 'LIBnn=lib' 'build_alias=x86_64-conda_cos6-linux-gnu' 'host_alias=x86_64-conda_cos6-linux-gnu' 'PKG_CONFIG_PATH=/home/fabrost/miniconda3/envs/spols200116/lib/pkgconfig' 'CC=x86_64-conda_cos6-linux-gnu-cc' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/fabrost/miniconda3/envs/spols200116/lib -Wl,-rpath-link,/home/fabrost/miniconda3/envs/spols200116/lib -L/home/fabrost/miniconda3/envs/spols200116/lib -Wl,-rpath-link,/home/fabrost/miniconda3/envs/spols200116/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/fabrost/miniconda3/envs/spols200116/include -Wl,-rpath-link,/home/fabrost/miniconda3/envs/spols200116/lib' 'CPP=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp' 'FC=x86_64-conda_cos6-linux-gnu-gfortran' 'CXX=x86_64-conda_cos6-linux-gnu-c++' 'CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix' 'OBJC=x86_64-conda_cos6-linux-gnu-cc'
## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk
AR = x86_64-conda_cos6-linux-gnu-ar
BLAS_LIBS = -lblas
C_VISIBILITY = -fvisibility=hidden
CC = x86_64-conda_cos6-linux-gnu-cc
CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/fabrost/miniconda3/envs/spols200116/include -Wl,-rpath-link,/home/fabrost/miniconda3/envs/spols200116/lib
CXX = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11
CXXCPP = $(CXX) -E
CXXFLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
CXXPICFLAGS = -fpic
CXX98 = x86_64-conda_cos6-linux-gnu-c++
CXX98FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
CXX98PICFLAGS = -fpic
CXX98STD = -std=gnu++98
CXX11 = x86_64-conda_cos6-linux-gnu-c++
CXX11FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = x86_64-conda_cos6-linux-gnu-c++
CXX14FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = x86_64-conda_cos6-linux-gnu-c++
CXX17FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
F_VISIBILITY = -fvisibility=hidden
## FC is the compiler used for all Fortran as from R 3.6.0
FC = x86_64-conda_cos6-linux-gnu-gfortran
FCFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix $(LTO)
FLIBS = -lgfortran -lm -lgomp -lquadmath -lpthread
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR = /usr/lib64/jvm/java/bin/jar
JAVA = /usr/lib64/jvm/java/bin/java
JAVAC = /usr/lib64/jvm/java/bin/javac
JAVAH = /home/fabrost/miniconda3/envs/spols200116/bin/javah
## JAVA_HOME might be used in the next three.
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /usr/lib64/jvm/java
JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JAVA_LIBS = -L$(JAVA_HOME)-11-openjdk-11/lib/server -ljvm
JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)-11-openjdk-11/lib/server
LAPACK_LIBS = -llapack
LDFLAGS = -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/fabrost/miniconda3/envs/spols200116/lib -Wl,-rpath-link,/home/fabrost/miniconda3/envs/spols200116/lib -L/home/fabrost/miniconda3/envs/spols200116/lib -Wl,-rpath-link,/home/fabrost/miniconda3/envs/spols200116/lib
## we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -L"$(R_HOME)/lib$(R_ARCH)" -lR
LIBS = -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -liconv -licuuc -licui18n
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
LTO =
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
RPATH_LDFLAGS = -Wl,-rpath,$(abs_top_builddir)/lib -Wl,-rpath,/home/fabrost/miniconda3/envs/spols200116/lib
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) $(RPATH_LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
OBJC = x86_64-conda_cos6-linux-gnu-cc
OBJCFLAGS = -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS =
OBJCXX =
R_ARCH =
RANLIB = x86_64-conda_cos6-linux-gnu-ranlib
SAFE_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/fabrost/miniconda3/envs/spols200116/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/fabrost/miniconda3/envs/spols200116=/usr/local/src/conda-prefix -msse2 -mfpmath=sse
SED = /home/fabrost/miniconda3/envs/spols200116/bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LD = $(CXX98) $(CXX98STD)
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = $(CC)
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS)
SHLIB_LIBADD =
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS =
STRIP_STATIC_LIB = x86_64-conda_cos6-linux-gnu-strip --strip-debug
STRIP_SHARED_LIB = x86_64-conda_cos6-linux-gnu-strip --strip-unneeded
TCLTK_CPPFLAGS = -I/home/fabrost/miniconda3/envs/spols200116/include -I/home/fabrost/miniconda3/envs/spols200116/include
TCLTK_LIBS = -L/home/fabrost/miniconda3/envs/spols200116/lib -ltcl8.6 -L/home/fabrost/miniconda3/envs/spols200116/lib -ltk8.6 -lX11
YACC = yacc
## Legacy settings: no longer used by R as of 3.6.0
## Setting FC often sets F77 (on Solaris make even if set)
## so must follow FC in this file.
F77 = x86_64-conda_cos6-linux-gnu-gfortran
FCPICFLAGS = -fpic
F77_VISIBILITY = -fvisibility=hidden
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared
SHLIB_OPENMP_FCFLAGS =
## for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "$(R_HOME)/lib$(R_ARCH)/libR.a" -Wl,--no-whole-archive $(BLAS_LIBS) $(FLIBS) $(LIBINTL) -lreadline $(LIBS)
## These are recorded as macros for legacy use in packages
## set on AIX, formerly for old glibc (-D__NO_MATH_INLINES)
R_XTRA_CFLAGS =
## was formerly set on HP-UX
R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG
## currently unset
R_XTRA_CXXFLAGS =
## used for gfortran in R > 3.6.0
R_XTRA_FFLAGS = -fno-optimize-sibling-calls
## SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
## SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CFLAGS = $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
ALL_CXXFLAGS = $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = -fno-optimize-sibling-calls $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## can be overridden by R CMD SHLIB
P_FCFLAGS = $(PKG_FFLAGS)
ALL_FCFLAGS = -fno-optimize-sibling-calls $(P_FCFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FCFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)
.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o
.c.o:
$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
@echo "making $@ from $<"
@$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.cc.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
$(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
@echo "making $@ from $<"
@x86_64-conda_cos6-linux-gnu-cc -MM $(ALL_CPPFLAGS) $< > $@
.mm.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
$(FC) $(ALL_FFLAGS) -c $< -o $@
## @FCFLAGS_f9x@ are flags needed to recognise the extensions
.f95.o:
$(FC) $(ALL_FCFLAGS) -c $< -o $@
.f90.o:
$(FC) $(ALL_FCFLAGS) -c $< -o $@
sessionInfo():
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: openSUSE Leap 15.1
Matrix products: default
BLAS/LAPACK: /home/fabrost/miniconda3/envs/spols200116/lib/libopenblasp-r0.3.6.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.1Unable to install leidenbase on Mac OS
Hi
I'm trying to install leidenbase, but can't do and get error.
The error occurs when I attempt to run the following code:
devtools::install_github('cole-trapnell-lab/leidenbase')
In file included from cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c:80:
cigraph/src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c:141:40: warning: unused variable 'tstart' [-Wunused-variable]
double one [2], zero [2], fjk [2], tstart ;
^
192 warnings and 3 errors generated.
make: *** [cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
- removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’
sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] ja_JP.UTF-8/ja_JP.UTF-8/ja_JP.UTF-8/C/ja_JP.UTF-8/ja_JP.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_1.2-18
loaded via a namespace (and not attached):
[1] rstudioapi_0.11 magrittr_1.5 usethis_1.6.1 devtools_2.3.1
[5] pkgload_1.1.0 lattice_0.20-38 R6_2.4.1 rlang_0.4.7
[9] fansi_0.4.1 tools_3.6.3 pkgbuild_1.1.0 grid_3.6.3
[13] sessioninfo_1.1.1 cli_2.0.2 withr_2.2.0 remotes_2.2.0
[17] ellipsis_0.3.1 assertthat_0.2.1 digest_0.6.25 rprojroot_1.3-2
[21] crayon_1.3.4 processx_3.4.3 BiocManager_1.30.10 callr_3.4.3
[25] fs_1.5.0 ps_1.3.3 curl_4.3 testthat_2.3.2
[29] memoise_1.1.0 glue_1.4.1 compiler_3.6.3 desc_1.2.0
[33] backports_1.1.8 prettyunits_1.1.1
This error occur in R version 3.6.3 and 4.0.2.
I already installed Xcode command line tools.
Thanks,
Masaya
no DESCRIPTION file for this package
For some reason I cannot install this package from devtools::install_github, probably due to curl being too old in Centos 7.3.
Anyway, I downloaded the package in zip and also git cloned the package, in the hope to install the package locally. In R-3.6.0, I got the following error message:
> devtools::install("leidenbase")
Error: Could not find package root.
> devtools::install_local("~/leidenbase-dev.zip")
Error: Failed to install 'leidenbase-dev.zip' from local:
Does not appear to be an R package (no DESCRIPTION)
For the 2nd error, shouldn't there be a DESCRIPTION for this R package? I'd appreciate it if you could add a DESCRIPTION file, or suggest an alternative way to finish the local installation.
Thanks!
compilation failed for package ‘leidenbase’
** If this is a question and not a bug report or enhancement request, please post to our google group at https://groups.google.com/forum/#!forum/monocle-3-users**
Describe the bug
Mac OS Catalina. Compilation failed for leidenbase.
Installed macports gcc9 +gfortran and installed new R.3.6.2. How do I make R look for the /opt/local/bin/gcc and fortran.
% which gcc
/opt/local/bin/gcc
% which gfortran
/opt/local/bin/gfortran
Error report:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [leidenbase.so] Error 1
ERROR: compilation failed for package ‘leidenbase’
- removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘/var/folders/wz/ycqjlndj0059y015qm0gxtc40000gp/T//Rtmp1bXrXC/file2ad55ff99a6/leidenbase_0.1.0.tar.gz’ had non-zero exit status
To Reproduce
The code that produced the bug:
devtools::install_github('cole-trapnell-lab/leidenbase')
traceback()
traceback()
8: stop(remote_install_error(remotes[[i]], e))
7: value[3L]
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
4: tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) {
stop(remote_install_error(remotes[[i]], e))
})
3: install_remotes(remotes, auth_token = auth_token, host = host,
dependencies = dependencies, upgrade = upgrade, force = force,
quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual,
build_vignettes = build_vignettes, repos = repos, type = type,
...)
2: pkgbuild::with_build_tools({
ellipsis::check_dots_used(action = getOption("devtools.ellipsis_action",
rlang::warn))
{
remotes <- lapply(repo, github_remote, ref = ref, subdir = subdir,
auth_token = auth_token, host = host)
install_remotes(remotes, auth_token = auth_token, host = host,
dependencies = dependencies, upgrade = upgrade, force = force,
quiet = quiet, build = build, build_opts = build_opts,
build_manual = build_manual, build_vignettes = build_vignettes,
repos = repos, type = type, ...)
}
}, required = FALSE)
1: devtools::install_github("cole-trapnell-lab/leidenbase")
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
sessionInfo():
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 rstudioapi_0.11 magrittr_1.5 usethis_1.5.1 devtools_2.2.1 pkgload_1.0.2 R6_2.4.1
[8] rlang_0.4.4 fansi_0.4.1 tools_3.6.2 pkgbuild_1.0.6 sessioninfo_1.1.1 cli_2.0.1 withr_2.1.2
[15] ellipsis_0.3.0 remotes_2.1.0 assertthat_0.2.1 digest_0.6.24 rprojroot_1.3-2 crayon_1.3.4 processx_3.4.2
[22] callr_3.4.2 fs_1.3.1 ps_1.3.2 curl_4.3 testthat_2.3.1 memoise_1.1.0 glue_1.3.1
[29] compiler_3.6.2 desc_1.2.0 backports_1.1.5 prettyunits_1.1.1
Additional context
Add any other context about the problem here.
issues when installing leidenbase on windows using rstudio
Hi, when using devtools::install_github('cole-trapnell-lab/leidenbase') to install leidenbase, I got the following error message:
"C:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA
1/R/R-401.2/include" -DNDEBUG -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION="1.1.2.9000" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DHAVE_GFORTRAN -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c -o cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.o
In file included from cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.c:63:
cigraph/src/igraph_blas_internal.h:33:10: fatal error: config.h: No such file or directory
#include "config.h"
^~~~~~~~~~
compilation terminated.
make: *** [C:/PROGRA1/R/R-401.2/etc/i386/Makeconf:222: cigraph/src/CHOLMOD/Supernodal/cholmod_super_numeric.o] Error 1
ERROR: compilation failed for package 'leidenbase'
- removing 'C:/Users/jimmy/OneDrive/Documents/R/win-library/4.0/leidenbase'
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘C:/Users/jimmy/AppData/Local/Temp/RtmpcD75OC/file32ac67414600/leidenbase_0.1.1.tar.gz’ had non-zero exit status
If I skip leidenbase and install Monocle3, it gives the same error message.
My sessioninfo after installing leidenbase from github:
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252attached base packages:
[1] stats graphics grDevices utils datasets methods baseother attached packages:
[1] Seurat_3.1.5loaded via a namespace (and not attached):
[1] nlme_3.1-148 tsne_0.1-3 fs_1.4.2 usethis_1.6.1 devtools_2.3.0 RcppAnnoy_0.0.16
[7] RColorBrewer_1.1-2 httr_1.4.1 rprojroot_1.3-2 sctransform_0.2.1 tools_4.0.2 backports_1.1.8
[13] R6_2.4.1 irlba_2.3.3 KernSmooth_2.23-17 uwot_0.1.8 lazyeval_0.2.2 colorspace_1.4-1
[19] withr_2.2.0 tidyselect_1.1.0 gridExtra_2.3 prettyunits_1.1.1 processx_3.4.3 curl_4.3
[25] compiler_4.0.2 cli_2.0.2 desc_1.2.0 plotly_4.9.2.1 scales_1.1.1 lmtest_0.9-37
[31] ggridges_0.5.2 callr_3.4.3 pbapply_1.4-2 rappdirs_0.3.1 stringr_1.4.0 digest_0.6.25
[37] pkgconfig_2.0.3 htmltools_0.5.0 sessioninfo_1.1.1 htmlwidgets_1.5.1 rlang_0.4.7 rstudioapi_0.11
[43] generics_0.0.2 zoo_1.8-8 jsonlite_1.7.0 ica_1.0-2 dplyr_1.0.0 magrittr_1.5
[49] patchwork_1.0.1 Matrix_1.2-18 Rcpp_1.0.5 munsell_0.5.0 fansi_0.4.1 ape_5.4
[55] reticulate_1.16 lifecycle_0.2.0 stringi_1.4.6 MASS_7.3-51.6 pkgbuild_1.0.8 Rtsne_0.15
[61] plyr_1.8.6 grid_4.0.2 parallel_4.0.2 listenv_0.8.0 ggrepel_0.8.2 crayon_1.3.4
[67] lattice_0.20-41 cowplot_1.0.0 splines_4.0.2 ps_1.3.3 pillar_1.4.6 igraph_1.2.5
[73] future.apply_1.6.0 reshape2_1.4.4 codetools_0.2-16 pkgload_1.1.0 leiden_0.3.3 glue_1.4.1
[79] BiocManager_1.30.10 remotes_2.1.1 data.table_1.12.8 png_0.1-7 vctrs_0.3.1 testthat_2.3.2
[85] gtable_0.3.0 RANN_2.6.1 purrr_0.3.4 tidyr_1.1.0 future_1.18.0 assertthat_0.2.1
[91] ggplot2_3.3.2 rsvd_1.0.3 survival_3.2-3 viridisLite_0.3.0 tibble_3.0.3 memoise_1.1.0
[97] cluster_2.1.0 globals_0.12.5 fitdistrplus_1.1-1 ellipsis_0.3.1 ROCR_1.0-11
Traceback:
10: stop(remote_install_error(remotes[[i]], e))
9: value[3L]
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) {
stop(remote_install_error(remotes[[i]], e))
})
5: install_remotes(remotes, auth_token = auth_token, host = host,
dependencies = dependencies, upgrade = upgrade, force = force,
quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual,
build_vignettes = build_vignettes, repos = repos, type = type,
...)
4: force(code)
3: withr::with_path(rtools_path(), code)
2: pkgbuild::with_build_tools({
ellipsis::check_dots_used(action = getOption("devtools.ellipsis_action",
rlang::warn))
{
remotes <- lapply(repo, github_remote, ref = ref, subdir = subdir,
auth_token = auth_token, host = host)
install_remotes(remotes, auth_token = auth_token, host = host,
dependencies = dependencies, upgrade = upgrade, force = force,
quiet = quiet, build = build, build_opts = build_opts,
build_manual = build_manual, build_vignettes = build_vignettes,
repos = repos, type = type, ...)
}
}, required = FALSE)
1: devtools::install_github("cole-trapnell-lab/leidenbase")
And Makeconf:
AR = $(BINPREF)ar
BLAS_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRblas
C_VISIBILITY =
CC =$(BINPREF)gcc $ (M_ARCH)
CFLAGS = -O2 -Wall $(DEBUGFLAG) -std=gnu99 -mfpmath=sse -msse2 -mstackrealign
CPICFLAGS =
CPPFLAGS =
CXX =$(BINPREF)g++ -std=gnu++11 $ (M_ARCH)
CXXCPP = $(CXX) -E
CXXFLAGS = -O2 -Wall $(DEBUGFLAG) -mfpmath=sse -msse2 -mstackrealign
CXXPICFLAGS =
#CXX98 =$(BINPREF)g++ $ (M_ARCH)
#CXX98FLAGS = -O2 -Wall $(DEBUGFLAG) -mfpmath=sse -msse2 -mstackrealign
#CXX98PICFLAGS =
#CXX98STD = -std=gnu++98
CXX11 =$(BINPREF)g++ $ (M_ARCH)
CXX11FLAGS = -O2 -Wall $(DEBUGFLAG) -mfpmath=sse -msse2 -mstackrealign
CXX11PICFLAGS =
CXX11STD = -std=gnu++11these settings are for gcc >= 8
CXX14 = $(CXX11)
CXX14FLAGS = $(CXX11FLAGS)
CXX14PICFLAGS =
CXX14STD = -std=gnu++14
CXX17 = $(CXX11)
CXX17FLAGS = $(CXX11FLAGS)
CXX17PICFLAGS =
CXX17STD = -std=gnu++17
CXX20 = $(CXX11)
CXX20FLAGS = $(CXX11FLAGS)
CXX20PICFLAGS =
CXX20STD = -std=gnu++2a
DYLIB_EXT = .dll
DYLIB_LD = $(DLL)
DYLIB_LDFLAGS = -shared
DYLIB_LINK =$(DYLIB_LD) $ (DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =unsupported on Windows
F_VISIBILITY =
FC is the compiler used for all Fortran as from R 3.6.0
FC =
$(BINPREF)gfortran $ (M_ARCH)
FCFLAGS = -O2 $(DEBUGFLAG) -mfpmath=sse -msse2 -mstackrealignadditional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
F77 =$(BINPREF)gfortran $ (M_ARCH)
F77_VISIBILITY =
FFLAGS = -O2 $(DEBUGFLAG) -mfpmath=sse -msse2 -mstackrealign
FLIBS = -lgfortran -lm -lquadmath
The install.out file is here
Thank you very much and any help will be greatly appreciated!
installation error on centos 6
Hi,
I was trying to install in centos 6 and encountered this error:
devtools::install_github('cole-trapnell-lab/leidenbase')
In file included from /usr/include/c++/4.8.2/cstdint:35:0, from leidenFindPartition.cpp:68: /usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support for the \ ^ In file included from leidenFindPartition.cpp:79:0: leidenFindPartition.h:32:33: error: ‘std::int32_t’ has not been declared std::int32_t numIter, ^ leidenFindPartition.cpp:91:28: error: ‘std::int32_t’ has not been declared std::int32_t numIter, ^ leidenFindPartition.cpp:99:53: error: ‘std::int32_t’ has not been declared double resolutionParameter, std::int32_t numIter, int *pstatus ); ^ leidenFindPartition.cpp:120:33: error: ‘std::int32_t’ has not been declared std::int32_t numIter, ^ leidenFindPartition.cpp: In function ‘int leidenFindPartition(igraph_t*, std::string, const std::vector<long unsigned int>*, const std::vector<double>*, const std::vector<long unsigned int>*, size_t, double, int, std::vector<long unsigned int>*, std::vector<double>*, std::vector<double>*, std::vector<double>*, double*, double*, double*, double*, int*)’: leidenFindPartition.cpp:133:3: error: ‘int32_t’ is not a member of ‘std’ std::int32_t iiter; ^ leidenFindPartition.cpp:133:3: note: suggested alternative: In file included from /usr/include/stdlib.h:314:0, from cigraph/include/igraph_memory.h:27, from cigraph/include/igraph.h:32, from leidenFindPartition.cpp:69: /usr/include/sys/types.h:196:1: note: ‘int32_t’ __intN_t (32, __SI__); ^ leidenFindPartition.cpp:133:16: error: expected ‘;’ before ‘iiter’ std::int32_t iiter; ^ leidenFindPartition.cpp:205:8: error: ‘iiter’ was not declared in this scope for( iiter = 0; iiter < numIter; ++iiter ) ^ leidenFindPartition.cpp: At global scope: leidenFindPartition.cpp:285:28: error: ‘std::int32_t’ has not been declared std::int32_t numIter, ^ leidenFindPartition.cpp:343:1: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] }; ^ leidenFindPartition.cpp:343:1: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] leidenFindPartition.cpp:343:1: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] leidenFindPartition.cpp:343:1: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] leidenFindPartition.cpp:343:1: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] leidenFindPartition.cpp:343:1: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] leidenFindPartition.cpp:354:57: error: ‘std::int32_t’ has not been declared double resolutionParameter, std::int32_t numIter, int *pstatus ) ^ make: *** [leidenFindPartition.o] Error 1 ERROR: compilation failed for package ‘leidenbase’ * removing ‘/camhpc/home/gzhang/R/x86_64-pc-linux-gnu-library/3.5/leidenbase’ Error: Failed to install 'leidenbase' from GitHub: (converted from warning) installation of package ‘/tmp/RtmpuO7rAd/file66d13137793b/leidenbase_0.1.0.tar.gz’ had non-zero exit status
Tried a few different ways, install from github, download the release tar.gz and install by install.packages("~/packages/0.1.0.tar.gz", type = 'source', repos = NULL), or R CMD INSTALL, all gave the same error.
Could you help?
Thanks.
Problem installing leidenbase on MacOS
Hello,
I don't manage to download liedenbase on my MAC.
Here are the info.
MacOS Mojave 10.14.6
cc (GCC) 4.8.5
c++ (GCC) 4.8.5
GNU Fortran (GCC) 4.8.5
R version 3.6.1
etc/Makeconf. Generated from Makeconf.in by configure.
${R_HOME}/etc/Makeconf
R was configured using the following call
(not including env. vars and site configuration)
configure 'CC=clang' 'CXX=clang++' 'OBJC=clang' 'CFLAGS=-Wall -g -O2' 'CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include' 'CXXFLAGS=-Wall -g -O2' 'OBJCFLAGS=-Wall -g -O2' 'FCFLAGS=-Wall -g -O2' 'F77FLAGS=-Wall -g -O2' '--enable-memory-profiling' '--x-libraries=/opt/X11/lib' '--enable-R-framework' 'PKG_CONFIG_PATH=/usr/lib/pkgconfig:/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig'
This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk
AR = ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY =
CC = clang
CFLAGS = -Wall -g -O2 $(LTO)
CPICFLAGS = -fPIC
CPPFLAGS = -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
CXX = clang++ -std=gnu++11
CXXCPP = $(CXX) -E
CXXFLAGS = -Wall -g -O2 $(LTO)
CXXPICFLAGS = -fPIC
CXX98 = clang++
CXX98FLAGS = -Wall -g -O2 $(LTO)
CXX98PICFLAGS = -fPIC
CXX98STD = -std=gnu++98
CXX11 = clang++
CXX11FLAGS = -Wall -g -O2 $(LTO)
CXX11PICFLAGS = -fPIC
CXX11STD = -std=gnu++11
CXX14 = clang++
CXX14FLAGS = -Wall -g -O2 $(LTO)
CXX14PICFLAGS = -fPIC
CXX14STD = -std=gnu++14
CXX17 = clang++
CXX17FLAGS = -Wall -g -O2 $(LTO)
CXX17PICFLAGS = -fPIC
CXX17STD = -std=gnu++17
CXX_VISIBILITY =
DYLIB_EXT = .dylib
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -fopenmp#
DYLIB_LINK =
ECHO = echo
ECHO_C = \c
ECHO_N =
ECHO_T =
F_VISIBILITY =
FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran
FCFLAGS = -Wall -g -O2 $(LTO)
additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -Wall -g -O2 $(LTO)
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
FPICFLAGS = -fPIC
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS = -framework Foundation
JAR = /usr/bin/jar
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVAH = /usr/bin/javah
JAVA_HOME might be used in the next three.
They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home
JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm
JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/server
LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack
LDFLAGS = -L/usr/local/lib
we only need this is if it is external, as otherwise link to R
LIBINTL= -Wl,-framework -Wl,CoreFoundation
LIBM =
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -F/Library/Frameworks/R.framework/.. -framework R
LIBS = -lpcre -llzma -lbz2 -lz -licucore -ldl -lm -liconv
needed by R CMD config
LIBnn = lib
LIBTOOL =
LTO =
needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -fopenmp
MAIN_LINK =
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
OBJC = clang
OBJCFLAGS = -Wall -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS = -lobjc
OBJCXX = clang++
R_ARCH =
RANLIB = ranlib
SAFE_FFLAGS = -Wall -g -O2 -msse2 -mfpmath=sse
SED = /usr/bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX98LD =
SHLIB_CXX98LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX11LD =
SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX14LD =
SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX17LD =
SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = $(CC)
SHLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress#
SHLIB_LIBADD =
We want to ensure libR is picked up from $(R_HOME)/lib
before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK =
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS = -fopenmp
STRIP_STATIC_LIB = strip -S
STRIP_SHARED_LIB = strip -x
TCLTK_CPPFLAGS = -I/usr/local/include -I/usr/local/include -I/opt/X11/include
TCLTK_LIBS = -L/usr/local/lib -ltcl8.6 -L/usr/local/lib -ltk8.6 -L/opt/X11/lib -lX11 -Wl,-weak-lXss -lXext
YACC = bison -y
Legacy settings: no longer used by R as of 3.6.0
Setting FC often sets F77 (on Solaris make even if set)
so must follow FC in this file.
F77 = gfortran
FCPICFLAGS = -fPIC
F77_VISIBILITY =
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_OPENMP_FCFLAGS = -fopenmp
for linking to libR.a
STATIC_LIBR = # "$(R_HOME)/lib$(R_ARCH)/libR.a"
These are recorded as macros for legacy use in packages
set on AIX, formerly for old glibc (-D__NO_MATH_INLINES)
R_XTRA_CFLAGS =
was formerly set on HP-UX
R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG
currently unset
R_XTRA_CXXFLAGS =
used for gfortran in R > 3.6.0
R_XTRA_FFLAGS =
SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CFLAGS =
ALL_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG
ALL_CXXFLAGS =
ALL_OBJCFLAGS =
ALL_OBJCXXFLAGS =
ALL_FFLAGS =
can be overridden by R CMD SHLIB
P_FCFLAGS = $(PKG_FFLAGS)
ALL_FCFLAGS =
LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS =
.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o
.c.o:
.c.d:
@echo "making
@$(CC) -MM
.cc.o:
.cpp.o:
.cc.d:
@echo "making
@$(CXX) -M
.cpp.d:
@echo "making
@$(CXX) -M
.m.o:
.m.d:
@echo "making
@clang -MM
.mm.o:
.M.o:
.f.o:
@FCFLAGS_f9x@ are flags needed to recognise the extensions
.f95.o:
.f90.o:
Warning in untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers
- installing to library ‘/Users/u0133753/opt/anaconda3/lib/R/library’
- installing source package ‘leidenbase’ ...
** using staged installation
checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
checking whether the C compiler works... no
configure: error: in/private/var/folders/sg/ygb24p6544b7nszkmtb4ksgx5zsxc8/T/Rtmpl04gET/R.INSTALL38912ba03861/leidenbase-0.1.0': configure: error: C compiler cannot create executables Seeconfig.log' for more details
ERROR: configuration failed for package ‘leidenbase’ - removing ‘/Users/u0133753/opt/anaconda3/lib/R/library/leidenbase’
- restoring previous ‘/Users/u0133753/opt/anaconda3/lib/R/library/leidenbase’
Could you help me?
Thank you!
Best wishes,
Aurélie
compilation failed for package 'leidenbase'
Hi @ctrapnell ,
Got a problem with the newest release. Any suggestion?
Regards,
Nelosn
> devtools::install_github('cole-trapnell-lab/leidenbase')
Downloading GitHub repo cole-trapnell-lab/leidenbase@master
√ checking for file 'C:\Users\KC\AppData\Local\Temp\RtmpGCd3rb\remotes56c2d24327\cole-trapnell-lab-leidenbase-d052373/DESCRIPTION' ...
- preparing 'leidenbase': (1.4s)
√ checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories (1.9s)
- building 'leidenbase_0.1.0.tar.gz'
Warning: file 'leidenbase/configure' did not have execute permissions: corrected
Warning: file 'leidenbase/src/cigraph/configure' did not have execute permissions: corrected
Installing package into ‘C:/Users/KC/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package 'leidenbase' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
*** arch - i386
C:/RBuildTools/3.5/mingw_32/bin/gfortran -O3 -mtune=generic -c cigraph/src/AMD/Source/amd.f -o cigraph/src/AMD/Source/amd.o
C:/RBuildTools/3.5/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config @CPPFLAGS@ @CFLAGS@ -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -O3 -Wall -std=gnu99 -mtune=generic -c cigraph/src/AMD/Source/amd_1.c -o cigraph/src/AMD/Source/amd_1.o
gcc.exe: error: @CPPFLAGS@: No such file or directory
gcc.exe: error: @CFLAGS@: No such file or directory
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/i386/Makeconf:208: cigraph/src/AMD/Source/amd_1.o] Error 1
ERROR: compilation failed for package 'leidenbase'
* removing 'C:/Users/KC/Documents/R/win-library/3.6/leidenbase'
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘C:/Users/KC/AppData/Local/Temp/RtmpGCd3rb/file56c4e624241/leidenbase_0.1.0.tar.gz’ had non-zero exit status
Error: package or namespace load failed for ‘leidenbase’ in dyn.load
Hi,
I installed leidenbase in R 4.3.1(ubuntu 18.04.6 LTS), errors occurred:
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgfortran.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgfortran.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libquadmath.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libquadmath.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgfortran.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgfortran.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libquadmath.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libquadmath.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libstdc++.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libstdc++.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgcc_s.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgcc_s.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgcc_s.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001
/usr/bin/ld: warning: /home/neurospine/anaconda3/lib/libgcc_s.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002
installing to /home/neurospine/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-leidenbase-0.1.9/00new/leidenbase/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘leidenbase’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/neurospine/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-leidenbase-0.1.9/00new/leidenbase/libs/leidenbase.so':
libgfortran.so.5: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
- removing ‘/home/neurospine/R/x86_64-pc-linux-gnu-library/4.3/leidenbase’
could anyone help me out? Appreciate! Details in attachment
install.out.txt
Unable to install Monocle 3 on MacOS Catalina
I am having difficulty with installing Monocle 3 on MacOS Catalina, Version 10.15.4.
Describe the bug
When I try to install leidenbase, R ends with an error that loops infinitely. I have attached screen shots from right before the loop begins, and after it begins.
To Reproduce
The error occurs when I attempt to run the following code:
devtools::install_github('cole-trapnell-lab/leidenbase')
Screenshots
sessionInfo():
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 dplyr_1.0.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 cellranger_1.1.0 compiler_3.6.3 pillar_1.4.4 prettyunits_1.1.1 remotes_2.1.1 tools_3.6.3
[8] testthat_2.3.2 digest_0.6.25 pkgbuild_1.0.8 pkgload_1.1.0 memoise_1.1.0 lifecycle_0.2.0 tibble_3.0.1
[15] pkgconfig_2.0.3 rlang_0.4.6 cli_2.0.2 rstudioapi_0.11 curl_4.3 withr_2.2.0 desc_1.2.0
[22] generics_0.0.2 fs_1.4.1 vctrs_0.3.1 devtools_2.3.0 rprojroot_1.3-2 tidyselect_1.1.0 glue_1.4.1
[29] R6_2.4.1 processx_3.4.2 fansi_0.4.1 sessioninfo_1.1.1 callr_3.4.3 purrr_0.3.4 magrittr_1.5
[36] backports_1.1.7 ps_1.3.3 ellipsis_0.3.1 usethis_1.6.1 assertthat_0.2.1 crayon_1.3.4
Additional context
Add any other context about the problem here.
Compilation error for cigraph/src/plfit/hzeta.c
Hi,
When attempting to install leidenbase, I'm encountering a compilation error for one of the C files. (edited this post to format as per the guidelines)
Computer system
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.4 LTS
Release: 18.04
Codename: bionic
R installation
I'm using R 4.0.2, via a module provided on an HPC cluster.
Excerpted lines from Makeconf:
CC = gcc
CFLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -I/app/software/GLPK/4.65-GCCcore-8.3.0/include -I/app/software/ImageMagick/7.0.9-5-GCCcore-8.3.0/include -I/app/software/GSL/2.6-GCC-8.3.0/include -I/app/software/UDUNITS/2.2.26-GCCcore-8.3.0/include -I/app/software/HDF5/1.10.5-gompi-2019b/include -I/app/software/ICU/65.1-GCCcore-8.3.0/include -I/app/software/libsndfile/1.0.28-GCCcore-8.3.0/include -I/app/software/FFTW/3.3.8-gompi-2019b/include -I/app/software/NLopt/2.6.1-GCCcore-8.3.0/include -I/app/software/GMP/6.1.2-GCCcore-8.3.0/include -I/app/software/libxml2/2.9.9-GCCcore-8.3.0/include -I/app/software/cURL/7.66.0-GCCcore-8.3.0/include -I/app/software/Tk/8.6.9-GCCcore-8.3.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.0.10-GCCcore-8.3.0/include -I/app/software/libjpeg-turbo/2.0.3-GCCcore-8.3.0/include -I/app/software/libpng/1.6.37-GCCcore-8.3.0/include -I/app/software/PCRE2/10.33-GCCcore-8.3.0/include -I/app/software/SQLite/3.29.0-GCCcore-8.3.0/include -I/app/software/zlib/1.2.11-GCCcore-8.3.0/include -I/app/software/XZ/5.2.4-GCCcore-8.3.0/include -I/app/software/bzip2/1.0.8-GCCcore-8.3.0/include -I/app/software/ncurses/6.1-GCCcore-8.3.0/include -I/app/software/libreadline/8.0-GCCcore-8.3.0/include -I/app/software/cairo/1.16.0-GCCcore-8.3.0/include -I/app/software/libGLU/9.0.1-GCCcore-8.3.0/include -I/app/software/Mesa/19.1.7-GCCcore-8.3.0/include -I/app/software/X11/20190717-GCCcore-8.3.0/include -I/app/software/ScaLAPACK/2.0.2-gompi-2019b/include -I/app/software/OpenBLAS/0.3.7-GCC-8.3.0/include
CXX = g++ -std=gnu++11
## Not used by anything in R, in particular not for the .cc.d rule
## but used via R CMD config by several packages
CXXCPP = $(CXX) -E
CXXFLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11FLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = g++
CXX14FLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = g++
CXX17FLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX20 = g++
CXX20FLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
CXX20PICFLAGS = -fpic
CXX20STD = -std=gnu++2a
CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
F_VISIBILITY = -fvisibility=hidden
## FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran
FCFLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -O2 -ftree-vectorize -march=native -fno-math-errno $(LTO)
FLIBS = -lgfortran
R sessionInfo
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/software/OpenBLAS/0.3.7-GCC-8.3.0/lib/libopenblas_haswellp-r0.3.7.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.2
Describe the error
I encounter the following compilation error when attempting to install via install_github("cole-trapnell-lab/leidenbase")
gcc -std=c99 -I"/app/software/R/4.0.2-foss-2019b/lib/R/include" -DNDEBUG -I/app/software/GLPK/4.65-GCCcore-8.3.0/include -I/app/software/ImageMagick/7.0.9-5-GCCcore-8.3.0/include -I/app/software/GSL/2.6-GCC-8.3.0/include -I/app/software/UDUNITS/2.2.26-GCCcore-8.3.0/include -I/app/software/HDF5/1.10.5-gompi-2019b/include -I/app/software/ICU/65.1-GCCcore-8.3.0/include -I/app/software/libsndfile/1.0.28-GCCcore-8.3.0/include -I/app/software/FFTW/3.3.8-gompi-2019b/include -I/app/software/NLopt/2.6.1-GCCcore-8.3.0/include -I/app/software/GMP/6.1.2-GCCcore-8.3.0/include -I/app/software/libxml2/2.9.9-GCCcore-8.3.0/include -I/app/software/cURL/7.66.0-GCCcore-8.3.0/include -I/app/software/Tk/8.6.9-GCCcore-8.3.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.0.10-GCCcore-8.3.0/include -I/app/software/libjpeg-turbo/2.0.3-GCCcore-8.3.0/include -I/app/software/libpng/1.6.37-GCCcore-8.3.0/include -I/app/software/PCRE2/10.33-GCCcore-8.3.0/include -I/app/software/SQLite/3.29.0-GCCcore-8.3.0/include -I/app/software/zlib/1.2.11-GCCcore-8.3.0/include -I/app/software/XZ/5.2.4-GCCcore-8.3.0/include -I/app/software/bzip2/1.0.8-GCCcore-8.3.0/include -I/app/software/ncurses/6.1-GCCcore-8.3.0/include -I/app/software/libreadline/8.0-GCCcore-8.3.0/include -I/app/software/cairo/1.16.0-GCCcore-8.3.0/include -I/app/software/libGLU/9.0.1-GCCcore-8.3.0/include -I/app/software/Mesa/19.1.7-GCCcore-8.3.0/include -I/app/software/X11/20190717-GCCcore-8.3.0/include -I/app/software/ScaLAPACK/2.0.2-gompi-2019b/include -I/app/software/OpenBLAS/0.3.7-GCC-8.3.0/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -O2 -ftree-vectorize -march=native -fno-math-errno -I/home/mstone/.conda/envs/py37/include/libxml2 -I/home/mstone/.conda/envs/py37/include -O2 -ftree-vectorize -march=native -fno-math-errno -I/home/mstone/.conda/envs/py37/include/libxml2 -I/home/mstone/.conda/envs/py37/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"0.8.2\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c cigraph/src/plfit/hzeta.c -o cigraph/src/plfit/hzeta.o
cigraph/src/plfit/hzeta.c: In function ‘hsl_sf_lnhzeta_deriv_tuple_e’:
cigraph/src/plfit/hzeta.c:598:24: error: ‘M_LN2’ undeclared (first use in this function); did you mean ‘M_LOG2E’?
hsl_sf_hZeta1(s,2.0,M_LN2,&hZeta1_value,&hZeta1_abserror,NULL);
^~~~~
M_LOG2E
cigraph/src/plfit/hzeta.c:598:24: note: each undeclared identifier is reported only once for each function it appears in
/app/software/R/4.0.2-foss-2019b/lib/R/etc/Makeconf:167: recipe for target 'cigraph/src/plfit/hzeta.o' failed
make: *** [cigraph/src/plfit/hzeta.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
Do you have any suggestions for how to fix this?
Thanks!
missing tag/release for leidenbase 0.1.2
The current latest commit (8c52ebc) provides leidenbase 0.1.2, but there's no corresponding tag/release in https://github.com/cole-trapnell-lab/leidenbase/tags or https://github.com/cole-trapnell-lab/leidenbase/releases, please fix?
problems with installing the leidenbase in R studio
MacOS m1 chip Big Sur install issue with cmath error
I am trying to install in Rstudio (R version 4.1.0) on M1 silicon MacOS Big Sur 11.4 using:
devtools::install_github('cole-trapnell-lab/leidenbase')
I get this error message, which makes it look like the cmath header is not working.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -I. -Icigraph/src -Icigraph/include -Icigraph/src/prpack -Ileidenalg/include -DUSING_R -DPRPACK_IGRAPH_SUPPORT -fPIC -Wall -g -O2 -c cigraph/src/DensityGrid.cpp -o cigraph/src/DensityGrid.o
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
using ::signbit;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
~~^
/usr/local/include/math.h:752:12: note: 'finite' declared here
extern int finite(double)
^
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
using ::isinf;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
using ::isnan;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
^
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
^
In file included from cigraph/src/DensityGrid.cpp:41:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:329:9: error: no member named 'isless' in the global namespace
using ::isless;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:330:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:331:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:332:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:333:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
~~^
13 errors generated.
make: *** [cigraph/src/DensityGrid.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/leidenbase’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/37/6b_9y9v11nzftf912bbhbhr00000gn/T//Rtmph3567G/file159343f7bb5fc/leidenbase_0.1.3.tar.gz’ had non-zero exit status
>
I have edited ~/.R/Makevars file using tricks here to "relink" SDK to the C++ compiler. Still not working.
I also tried updating Xcode, deleting and redownloading Xcode, and deleting and redownloading CommandLineTools.
(base) Mackenzies-MacBook-Pro:Resources Mack$ pwd
/Library/Frameworks/R.framework/Resources
(base) Mackenzies-MacBook-Pro:Resources Mack$ find . -name "Makeconf*"
./etc/Makeconf
(base) Mackenzies-MacBook-Pro:Resources Mack$ nano ./etc/Makeconf
GNU nano 2.0.6 File: ./etc/Makeconf
SHLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
## used for standard packages
SHLIB_LDFLAGS_R = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
SHLIB_LIBADD =
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS =
SHLIB_OPENMP_CXXFLAGS =
SHLIB_OPENMP_FFLAGS =
STRIP_STATIC_LIB = strip -S
STRIP_SHARED_LIB = strip -x
TCLTK_CPPFLAGS = -I/usr/local/include -I/usr/local/include -I/opt/X11/include
TCLTK_LIBS = -L/usr/local/lib -ltcl8.6 -L/usr/local/lib -ltk8.6 -L/opt/X11/lib -lX11 -Wl,-weak-lXss -lXext
YACC = bison -y
## for linking to libR.a
STATIC_LIBR = # "$(R_HOME)/lib$(R_ARCH)/libR.a" $(BLAS_LIBS) $(FLIBS) $(LIBINTL) -lreadline -lncurses $(LIBS)
## These are recorded as macros for legacy use in packages
## set on AIX, formerly for old glibc (-D__NO_MATH_INLINES)
R_XTRA_CFLAGS =
## was formerly set on HP-UX
R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG
## currently unset
R_XTRA_CXXFLAGS =
## used for gfortran in R > 3.6.0
R_XTRA_FFLAGS = -fno-optimize-sibling-calls
## SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
## SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CFLAGS = $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
ALL_CXXFLAGS = $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = -fno-optimize-sibling-calls $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## can be overridden by R CMD SHLIB
P_FCFLAGS = $(PKG_FFLAGS)
ALL_FCFLAGS = -fno-optimize-sibling-calls $(P_FCFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FCFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR) $(LIBINTL)
.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o
.c.o:
$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
@echo "making $@ from $<"
@$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.cc.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
$(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
@echo "making $@ from $<"
@$(OBJC) -MM $(ALL_CPPFLAGS) $< > $@
.mm.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
$(FC) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
$(FC) $(ALL_FCFLAGS) -c $< -o $@
.f90.o:
$(FC) $(ALL_FCFLAGS) -c $< -o $@
Here is my current ~/.R/Makevars file:
CC=clang
CXX=clang++
CXXFLAGS= -O3 -pedantic -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
Here are more details on /usr/bin/clang:
Apple clang version 12.0.5 (clang-1205.0.22.11)
Target: x86_64-apple-darwin20.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
/usr/bin/clang++:
clang++ --version
Apple clang version 12.0.5 (clang-1205.0.22.11)
Target: x86_64-apple-darwin20.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
/usr/bin/gcc:
gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.5 (clang-1205.0.22.11)
Target: x86_64-apple-darwin20.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
/usr/local/bin/gfortran:
gfortran --version
GNU Fortran (GCC) 6.1.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Thanks in advance for advice or workarounds.
Test failures with the development version of igraph
We're changing the layout of igraph objects. This leads to check failures in your package, see https://github.com/igraph/rigraph/blob/f-igraph-t-idx-revdepcheck/revdep/problems.md and igraph/rigraph#789 for details.
To reproduce, please install the development version of igraph via
# install.packages("pak")
pak::pak("igraph/rigraph")and run R CMD check on your package.
We plan to release an igraph update on June 12, two weeks from now. Can you please send an update to CRAN that fixes the checks?
This package seems to use its own copy of igraph. The error happens in R_SEXP_to_igraph() which still assumes the old format. Please retrieve an edgelist on the R side and construct your igraph object on the C/C++ side.
Happy to help.
leidenbase not installed in windows 10 x64
Hello,
I am currently using windows 10 and trying to install leidenbase.
However, i keep getting the same error
and this is my R sessioninfo
i installed igraph manually just in case but still having error on 'igraph' compilation.
i think source version of igraph is not working for me.
is there any way to solve this problem?
Thank you!
make: gfortran: Permission denied
Trying to install leidenbase in R, but fail with following message:
make: gfortran: Permission denied
make: *** [arpack/dgetv0.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
- removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/leidenbase’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/z5/fnjct4t12nv2_w0qv5k2m9jm0000gn/T//RtmpHQzNci/filead27b3930b4/leidenbase_0.1.3.tar.gz’ had non-zero exit status
gfortran I installed:
which gfortran
/usr/local/gfortran/bin/gfortran
install monocle3 on R version4.0.1
devtools::install_github('cole-trapnell-lab/leidenbase')
Error: Failed to install 'unknown package' from GitHub:
Peer reports incompatible or unsupported protocol version.
devtools::install_github('cole-trapnell-lab/monocle3')
Error: Failed to install 'unknown package' from GitHub:
error: unknown type name ‘IGRAPH_THREAD_LOCAL’
When I install it on a Ubuntu server, I came across the error:
In file included from cigraph/src/adjlist.c:27:
cigraph/src/igraph_interrupt_internal.h:42:8: error: unknown type name ‘IGRAPH_THREAD_LOCAL’
and thus: ERROR: compilation failed for package ‘leidenbase’
sessionInfo:
version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.3.2 usethis_2.0.1 SeuratData_0.2.1 SeuratObject_4.0.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lattice_0.20-41 listenv_0.8.0 prettyunits_1.1.1 ps_1.6.0 assertthat_0.2.1
[7] rprojroot_2.0.2 digest_0.6.27 utf8_1.1.4 parallelly_1.23.0 R6_2.5.0 plyr_1.8.6
[13] ggplot2_3.3.3 pillar_1.5.0 rlang_0.4.10 rstudioapi_0.13 callr_3.5.1 Matrix_1.3-2
[19] desc_1.2.0 stringr_1.4.0 munsell_0.5.0 sctransform_0.3.2 compiler_4.0.4 pkgconfig_2.0.3
[25] pkgbuild_1.2.0 globals_0.14.0 tidyselect_1.1.0 tibble_3.1.0 gridExtra_2.3 codetools_0.2-18
[31] matrixStats_0.58.0 fansi_0.4.2 future_1.21.0 crayon_1.4.1 dplyr_1.0.4 withr_2.4.1
[37] MASS_7.3-53 rappdirs_0.3.3 grid_4.0.4 gtable_0.3.0 lifecycle_1.0.0 magrittr_2.0.1
[43] scales_1.1.1 future.apply_1.7.0 cli_2.3.1 stringi_1.5.3 cachem_1.0.4 reshape2_1.4.4
[49] fs_1.5.0 remotes_2.2.0 testthat_3.0.2 ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.6
[55] tools_4.0.4 glue_1.4.2 purrr_0.3.4 processx_3.4.5 pkgload_1.2.0 parallel_4.0.4
[61] fastmap_1.1.0 colorspace_2.0-0 sessioninfo_1.1.1 memoise_2.0.0
Installation problem on MacOS: make: 77: No such file or directory
I am trying to install monocl3 on a Mac. I am getting the following error
** libs
77 -fPIC -Wall -g -O2 -c cigraph/src/AMD/Source/amd.f -o cigraph/src/AMD/Source/amd.o
make: 77: No such file or directory
make: *** [cigraph/src/AMD/Source/amd.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
I have installed the gfortran
gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin16/6.3.0/lto-wrapper
Target: x86_64-apple-darwin16
Configured with: ../gcc-6.3.0/configure --prefix=/usr/local/gfortran --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin16 --with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 --with-mpfr=/Users/fx/devel/gcc/deps-static/x86_64 --with-mpc=/Users/fx/devel/gcc/deps-static/x86_64 --with-isl=/Users/fx/devel/gcc/deps-static/x86_64
Thread model: posix
gcc version 6.3.0 (GCC)
Please let me know what am I missing.
Thanks
Hena
Screenshots
sessionInfo():
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq2_1.26.0 SummarizedExperiment_1.16.1 DelayedArray_0.12.2 BiocParallel_1.20.1
[5] matrixStats_0.56.0 Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[9] IRanges_2.20.2 S4Vectors_0.24.3 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 ellipsis_0.3.0 rprojroot_1.3-2 htmlTable_1.13.3 XVector_0.26.0
[6] fs_1.4.1 base64enc_0.1-3 rstudioapi_0.11 remotes_2.1.1 bit64_0.9-7
[11] AnnotationDbi_1.48.0 fansi_0.4.1 codetools_0.2-16 splines_3.6.2 geneplotter_1.64.0
[16] knitr_1.28 pkgload_1.0.2 ade4_1.7-15 Formula_1.2-3 jsonlite_1.6.1
[21] phyloseq_1.30.0 annotate_1.64.0 cluster_2.1.0 png_0.1-7 BiocManager_1.30.10
[26] compiler_3.6.2 backports_1.1.6 assertthat_0.2.1 Matrix_1.2-18 lazyeval_0.2.2
[31] cli_2.0.2 acepack_1.4.1 htmltools_0.4.0 prettyunits_1.1.1 tools_3.6.2
[36] igraph_1.2.5 gtable_0.3.0 glue_1.4.0 GenomeInfoDbData_1.2.2 reshape2_1.4.3
[41] dplyr_0.8.5 Rcpp_1.0.4 vctrs_0.2.4 Biostrings_2.54.0 multtest_2.42.0
[46] ape_5.3 nlme_3.1-145 iterators_1.0.12 xfun_0.12 stringr_1.4.0
[51] ps_1.3.2 testthat_2.3.2 lifecycle_0.2.0 devtools_2.2.2 XML_3.99-0.3
[56] zlibbioc_1.32.0 MASS_7.3-51.5 scales_1.1.0 biomformat_1.14.0 rhdf5_2.30.1
[61] RColorBrewer_1.1-2 curl_4.3 yaml_2.2.1 memoise_1.1.0 gridExtra_2.3
[66] ggplot2_3.3.0 rpart_4.1-15 latticeExtra_0.6-29 stringi_1.4.6 RSQLite_2.2.0
[71] genefilter_1.68.0 desc_1.2.0 foreach_1.5.0 checkmate_2.0.0 permute_0.9-5
[76] pkgbuild_1.0.6 rlang_0.4.5 pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-41
[81] purrr_0.3.3 Rhdf5lib_1.8.0 htmlwidgets_1.5.1 bit_1.1-15.2 tidyselect_1.0.0
[86] processx_3.4.2 plyr_1.8.6 magrittr_1.5 R6_2.4.1 Hmisc_4.4-0
[91] DBI_1.1.0 pillar_1.4.3 foreign_0.8-76 withr_2.1.2 mgcv_1.8-31
[96] survival_3.1-11 RCurl_1.98-1.1 nnet_7.3-13 tibble_3.0.0 crayon_1.3.4
[101] usethis_1.5.1 jpeg_0.1-8.1 locfit_1.5-9.4 grid_3.6.2 data.table_1.12.8
[106] blob_1.2.1 callr_3.4.3 vegan_2.5-6 digest_0.6.25 xtable_1.8-4
[111] munsell_0.5.0 sessioninfo_1.1.1
Unable to install leidenbase
Hi,
I am trying to install monocle3 on RStudio and have to install leidenbase. I executed the command 'devtools::install_github('cole-trapnell-lab/leidenbase')', but get an error:
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c arpack/dgetv0.f -o arpack/dgetv0.o
gfortran-4.2: error trying to exec '/usr/local/bin/i686-apple-darwin8-gfortran-4.2': execvp: Bad CPU type in executable
make: *** [arpack/dgetv0.o] Error 255
ERROR: compilation failed for package ‘leidenbase’
- removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/leidenbase’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/r9/8x1bj6xx6q1cwbfjl8tzbqch0000gn/T//Rtmp0TQxGN/file69096e6c6a19/leidenbase_0.1.3.tar.gz’ had non-zero exit status
Failed to install leidenbase
Hello,
I have tried for many times but still failed to install the leidenbase package. Can you please help me out? Thank you very much.
My system is MacOS Big Sur Version 11.4.
gcc information:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.5 (clang-1205.0.22.11)
Target: x86_64-apple-darwin20.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
gfortran information
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin19/10.2.0/lto-wrapper
Target: x86_64-apple-darwin19
Configured with: ../gcc-10.2.0/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/build_package/deps --with-isl=/Users/fx/devel/gcc/build_package/deps --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin19 --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 10.2.0 (GCC)
R was installed via a package from CRAN. R version:
version
_
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 1.0
year 2021
month 05
day 18
svn rev 80317
language R
version.string R version 4.1.0 (2021-05-18)
nickname Camp Pontanezen
Makeconf information:
CC = clang -mmacosx-version-min=10.13
CFLAGS = -Wall -g -O2 $(LTO)
CPICFLAGS = -fPIC
CPPFLAGS = -I/usr/local/include
CXX = clang++ -mmacosx-version-min=10.13 -std=gnu++14
CXXFLAGS = -Wall -g -O2 $(LTO)
CXXPICFLAGS = -fPIC
CXX11 = clang++ -mmacosx-version-min=10.13
CXX11FLAGS = -Wall -g -O2 $(LTO)
CXX11PICFLAGS = -fPIC
CXX11STD = -std=gnu++11
CXX14 = clang++ -mmacosx-version-min=10.13
CXX14FLAGS = -Wall -g -O2 $(LTO)
CXX14PICFLAGS = -fPIC
CXX14STD = -std=gnu++14
CXX17 = clang++ -mmacosx-version-min=10.13
CXX17FLAGS = -Wall -g -O2 $(LTO)
CXX17PICFLAGS = -fPIC
CXX17STD = -std=gnu++17
CXX20 = clang++ -mmacosx-version-min=10.13
CXX20FLAGS = -Wall -g -O2 $(LTO)
CXX20PICFLAGS = -fPIC
CXX20STD = -std=gnu++2a
CXX_VISIBILITY =
DYLIB_EXT = .dylib
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress#
should be used by packges for dylibs, but at the time of writing was not
DYLIB_LINK =
ECHO = echo
ECHO_C = \c
ECHO_N =
ECHO_T =
F_VISIBILITY =
FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran -mmacosx-version-min=10.13
FCFLAGS = -Wall -g -O2 $(LTO_FC)
additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -Wall -g -O2 $(LTO_FC)
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
R sessionInfo
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 pillar_1.6.1 BiocManager_1.30.16 prettyunits_1.1.1
[5] remotes_2.4.0 tools_4.1.0 testthat_3.0.3 pkgbuild_1.2.0
[9] pkgload_1.2.1 memoise_2.0.0 lifecycle_1.0.0 tibble_3.1.2
[13] lattice_0.20-44 pkgconfig_2.0.3 rlang_0.4.11 Matrix_1.3-4
[17] rstudioapi_0.13 cli_2.5.0 curl_4.3.1 fastmap_1.1.0
[21] withr_2.4.2 dplyr_1.0.7 desc_1.3.0 generics_0.1.0
[25] fs_1.5.0 vctrs_0.3.8 devtools_2.4.2 rprojroot_2.0.2
[29] grid_4.1.0 tidyselect_1.1.1 glue_1.4.2 R6_2.5.0
[33] processx_3.5.2 fansi_0.5.0 sessioninfo_1.1.1 callr_3.7.0
[37] purrr_0.3.4 tidyr_1.1.3 magrittr_2.0.1 ps_1.6.0
[41] ellipsis_0.3.2 usethis_2.0.1 utf8_1.2.1 cachem_1.0.5
[45] crayon_1.4.1
error
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘leidenbase’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so, 6): Symbol not found: _GOMP_barrier
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so
Error: loading failed
Execution halted
ERROR: loading failed
- removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/leidenbase’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/n2/xwhyx56d1hn62lnfssylsls00000gn/T//RtmpN1DuwL/file23d70ed2840/leidenbase_0.1.3.tar.gz’ had non-zero exit status
install.out file
install.out.zip
Thank you very much!
Longfei
ERROR: compilation failed for package 'leidenbase'
Hi, brgew
An error occured when I installed cole-trapnell-lab/leidenbase. R said this:
** libs
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c cigraph/src/AMD/Source/amd.f -o cigraph/src/AMD/Source/amd.o
C:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config @CPPFLAGS@ @CFLAGS@ -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION="1.1.2.9000" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -O2 -Wall -std=gnu99 -mtune=generic -c cigraph/src/AMD/Source/amd_1.c -o cigraph/src/AMD/Source/amd_1.o
gcc.exe: error: @CPPFLAGS@: No such file or directory
gcc.exe: error: @CFLAGS@: No such file or directory
make: *** [C:/PROGRA1/R/R-361.1/etc/x64/Makeconf:208: cigraph/src/AMD/Source/amd_1.o] Error 1
ERROR: compilation failed for package 'leidenbase'
- removing 'C:/Program Files/R/R-3.6.1/library/leidenbase'
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘C:/Users/ADMINI~1/AppData/Local/Temp/RtmpOsRXL5/file2b585f484884/leidenbase_0.1.0.tar.gz’ had non-zero exit status
OS on my PC is win10. and R-3.6.1\etc\x64\Makeconf is:
AR = $(BINPREF)ar
BLAS_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRblas
C_VISIBILITY =
CC =
CFLAGS = -O2 -Wall $(DEBUGFLAG) -std=gnu99 -mtune=generic
CPICFLAGS =
CPPFLAGS =
CXX =
CXXCPP = $(CXX) -E
CXXFLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=generic
CXXPICFLAGS =
CXX98 =
CXX98FLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=generic
CXX98PICFLAGS =
CXX98STD = -std=gnu++98
CXX11 =
CXX11FLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=generic
CXX11PICFLAGS =
CXX11STD = -std=gnu++11
CXX14 =
CXX14FLAGS =
CXX14PICFLAGS =
CXX14STD =
CXX17 =
CXX17FLAGS =
CXX17PICFLAGS =
CXX17STD =
DYLIB_EXT = .dll
DYLIB_LD = $(DLL)
DYLIB_LDFLAGS = -shared
DYLIB_LINK =
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
I want to konw how to solve this problem, thank you very much.
Can't install leidenbase and monocle3
Hi
I'm trying to install monocle3 in Mac OSX 11.1
There are some issues that happened.
I can't install leidenbase and monocle3.
I have installed Xcode command line tool, the version is following:
=== Xcode 12.3 ===
- '''Xcode''': Build version 12C33
- '''clang''': Apple clang version 12.0.0 (clang-1200.0.32.28)%
The clang is the following:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.28)
Target: x86_64-apple-darwin20.2.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
I have installed gfortran. The gfortran version is the following by typing "gfortran --version" in the terminal :
myname@myname-MacBook-Pro ~ % gfortran --version
zsh: bad CPU type in executable: gfortran.
I downloaded gfortran from "https://github.com/fxcoudert/gfortran-for-macOS/releases", and I downloaded the version as "gfortran 11-experimental-2 for ARM Big Sur (macOS 11)". It seems like that is the main problem.
The code is the following :
devtools::install_github('cole-trapnell-lab/leidenbase'), the same as 'monocle3'
**> devtools::install_github('cole-trapnell-lab/leidenbase')
Downloading GitHub repo cole-trapnell-lab/leidenbase@HEAD
✓ checking for file ‘/private/var/folders/9h/33hhq6ks2qx5gzh2dmksfcxc0000gn/T/Rtmpaa9c6h/remotes76017d793fcd/cole-trapnell-lab-leidenbase-8c52ebc/DESCRIPTION’ ...
─ preparing ‘leidenbase’: (441ms)
✓ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories (633ms)
─ building ‘leidenbase_0.1.2.tar.gz’
- installing source package ‘leidenbase’ ...
** using staged installation
checking for gcc... clang -mmacosx-version-min=10.13
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++11 -E
checking for rintf... yes
checking for finite... yes
checking for expm1... yes
checking for rint... yes
checking for log2... yes
checking for logbl... yes
checking for snprintf... yes
checking for log1p... yes
checking for round... yes
checking for fmin... yes
checking for stpcpy... yes
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether stpcpy is declared... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking net/if.h usability... yes
checking net/if.h presence... yes
checking for net/if.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking net/if_dl.h usability... yes
checking net/if_dl.h presence... yes
checking for net/if_dl.h... yes
checking sys/sockio.h usability... yes
checking sys/sockio.h presence... yes
checking for sys/sockio.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking for struct sockaddr.sa_len... yes
checking for xml2-config... /usr/bin/xml2-config
checking for xmlSAXUserParseFile in -lxml2... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for __gmpz_add in -lgmp... yes
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
configure: creating ./config.status
config.status: creating src/Makevars.tmp
config.status: creating src/Makevars
=== configuring in src/cigraph (/private/var/folders/9h/33hhq6ks2qx5gzh2dmksfcxc0000gn/T/RtmpgrVicP/R.INSTALL9c6714bbaa39/leidenbase/src/cigraph)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
checking for gcc... clang -mmacosx-version-min=10.13
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether we are using the GNU Fortran compiler... no
checking whether gfortran -mmacosx-version-min=10.13 accepts -g... no
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++11 -E
checking for rintf... yes
checking for finite... yes
checking for expm1... yes
checking for rint... yes
checking for log2... yes
checking for logbl... yes
checking for snprintf... yes
checking for log1p... yes
checking for round... yes
checking for fmin... yes
checking for stpcpy... yes
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether stpcpy is declared... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking net/if.h usability... yes
checking net/if.h presence... yes
checking for net/if.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking net/if_dl.h usability... yes
checking net/if_dl.h presence... yes
checking for net/if_dl.h... yes
checking sys/sockio.h usability... yes
checking sys/sockio.h presence... yes
checking for sys/sockio.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking for struct sockaddr.sa_len... yes
checking for xml2-config... /usr/bin/xml2-config
checking for xmlSAXUserParseFile in -lxml2... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for __gmpz_add in -lgmp... yes
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
configure: creating ./config.status
config.status: creating src/config.h
** libs
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c cigraph/src/AMD/Source/amd.f -o cigraph/src/AMD/Source/amd.o
make: gfortran: Bad CPU type in executable
make: *** [cigraph/src/AMD/Source/amd.o] Error 1
ERROR: compilation failed for package ‘leidenbase’ - removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘/var/folders/9h/33hhq6ks2qx5gzh2dmksfcxc0000gn/T//Rtmpaa9c6h/file7601234bec16/leidenbase_0.1.2.tar.gz’ had non-zero exit status**
Thank you very much.
Build fail on R 4.4
I am getting the following error when compiling leidenbase from source
leidenbase/leidenFindPartitionR2C.cpp: In function ‘void R_leidenbase_error_handler(const char*, const char*, int, int)’:
leidenbase/leidenFindPartitionR2C.cpp:85:9: error: format not a string literal and no format arguments [-Werror=format-security]
85 | error(error_string);
| ^~~~~~~~~~~~
cc1plus: some warnings being treated as errors
make: *** [/usr/lib/R/etc/Makeconf:204: leidenbase/leidenFindPartitionR2C.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
* removing ‘/home/ygrabovska/R/x86_64-pc-linux-gnu-library/4.4/leidenbase’
* restoring previous ‘/home/ygrabovska/R/x86_64-pc-linux-gnu-library/4.4/leidenbase’
Warning message:
In i.p(...) :
installation of package ‘/tmp/Rtmphbs29D/file463364a1a3f1/leidenbase_0.1.25.tar.gz’ had non-zero exit status
I am running WSL2 Ubuntu LTS 22.04
C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
Could you suggest anything to try?
Problem installing leidenbase
Here's my info:
MacBookPro
MacOS version 10.15.1 (Catalina)
gfortran Fortran compiler
R Version 3.6.1
R Studio Version 1.1.463
Here's the error:
devtools::install_github('cole-trapnell-lab/leidenbase')
Downloading GitHub repo cole-trapnell-lab/leidenbase@master
✔ checking for file ‘/private/var/folders/h0/dw38ln8n6fqglfg2zvsyzwpw0000gn/T/RtmpEtfmUd/remotesa8254f7c592b/cole-trapnell-lab-leidenbase-c22a7d0/DESCRIPTION’ ...
─ preparing ‘leidenbase’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories (563ms)
─ building ‘leidenbase_0.1.0.tar.gz’
- installing source package ‘leidenbase’ ...
** using staged installation
checking for gcc... clang
checking whether the C compiler works... no
configure: error: in/private/var/folders/h0/dw38ln8n6fqglfg2zvsyzwpw0000gn/T/RtmpwTqpjF/R.INSTALLaa882e60489e/leidenbase': configure: error: C compiler cannot create executables Seeconfig.log' for more details
ERROR: configuration failed for package ‘leidenbase’ - removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
(converted from warning) installation of package ‘/var/folders/h0/dw38ln8n6fqglfg2zvsyzwpw0000gn/T//RtmpEtfmUd/filea82544aa431f/leidenbase_0.1.0.tar.gz’ had non-zero exit status
Making 'packages.html' ... done
Any help resolving this would be appreciated.
Thanks,
Oscar
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