unable to compile

[baj12]

Hi,

I am running into problems when trying to install now.
I had to switch to the new R version (4.02)

Please see below for details.

I assume that you have tested and it is working on your side. The first thing that comes to mind is the R version since there were quite a few changes. Did you test on 4.02?

Thx

Bernd

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

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

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] edgeR_3.30.3 limma_3.44.3

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 compiler_4.0.2 cytolib_2.0.3 remotes_2.1.1
[5] prettyunits_1.1.1 tools_4.0.2 testthat_2.3.2 digest_0.6.25
[9] packrat_0.5.0 pkgbuild_1.1.0 pkgload_1.1.0 memoise_1.1.0
[13] lattice_0.20-41 rlang_0.4.7 cli_2.0.2 rstudioapi_0.11
[17] curl_4.3 parallel_4.0.2 withr_2.2.0 fs_1.4.2
[21] desc_1.2.0 devtools_2.3.0 locfit_1.5-9.4 stats4_4.0.2
[25] rprojroot_1.3-2 grid_4.0.2 glue_1.4.1 Biobase_2.48.0
[29] R6_2.4.1 processx_3.4.3 fansi_0.4.1 sessioninfo_1.1.1
[33] RProtoBufLib_2.0.0 callr_3.4.3 magrittr_1.5 usethis_1.6.1
[37] backports_1.1.8 ps_1.3.3 matrixStats_0.56.0 ellipsis_0.3.1
[41] BiocGenerics_0.34.0 assertthat_0.2.1 flowCore_2.0.1 RcppParallel_5.0.2
[45] crayon_1.3.4

devtools::install_github("RausellLab/CelliD")
Downloading GitHub repo RausellLab/CelliD@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: Seurat (3.1.5 -> 3.2.0 ) [CRAN]
5: deldir (0.1-25 -> 0.1-28) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
3
✓ checking for file ‘/private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/RtmpGN7OPb/remotes34125c098528/RausellLab-CelliD-7bf1702/DESCRIPTION’ ...
─ preparing ‘CellID’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
─ installing source package ‘CellID’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dist.cpp -o dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mca.cpp -o mca.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c order.cpp -o order.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CellID.so RcppExports.o dist.o mca.o order.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
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'
installing to /private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/Rtmpbrly0X/Rinst35a1755dcc13/00LOCK-CellID/00new/CellID/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 13741 Done echo 'tools:::.install_packages()'
13742 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'CellID' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
E> installing to /private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/Rtmpbrly0X/Rinst35a1755dcc13/00LOCK-CellID/00new/CellID/libs
E> ** R
E> ** data
E> *** moving datasets to lazyload DB
E> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 13741 Done echo 'tools:::.install_packages()'
E> 13742 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
E> -----------------------------------
E> ERROR: package installation failed

devtools::install_github("RausellLab/CelliD",keep_outputs=T)
Downloading GitHub repo RausellLab/CelliD@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: Seurat (3.1.5 -> 3.2.0 ) [CRAN]
5: deldir (0.1-25 -> 0.1-28) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
3
✓ checking for file ‘/private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/RtmpGN7OPb/remotes3412670de24/RausellLab-CelliD-7bf1702/DESCRIPTION’ (529ms)
─ preparing ‘CellID’: (512ms)
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
─ installing source package ‘CellID’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dist.cpp -o dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mca.cpp -o mca.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c order.cpp -o order.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CellID.so RcppExports.o dist.o mca.o order.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
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'
installing to /private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/RtmpOJcnHq/Rinst3bbf3b816b17/00LOCK-CellID/00new/CellID/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 15307 Done echo 'tools:::.install_packages()'
15308 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'CellID' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
E> installing to /private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/RtmpOJcnHq/Rinst3bbf3b816b17/00LOCK-CellID/00new/CellID/libs
E> ** R
E> ** data
E> *** moving datasets to lazyload DB
E> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 15307 Done echo 'tools:::.install_packages()'
E> 15308 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
E> -----------------------------------
E> ERROR: package installation failed
Error in validate_signal_args(msg, type, call, .subclass) :
unused arguments (call, .subclass)

[Cortalak]

Hi, I haven't tested R version 4.02 explicitly myself but got some feedback that it indeed works.
I suspect more a problem of fortran library not recognized by MAC OS or not installed which is often the case with package having dependencies with RcppArmadillo.

E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
E> installing to /private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/RtmpOJcnHq/Rinst3bbf3b816b17/00LOCK-CellID

Please refer to installation issues in the read me file pointing at this link.

I will nonetheless test on 4.0.2 now

Best

[Cortalak]

On a sidenote to check if it is really a fortran problem, you can try to install packages like quantreg. If it fails with similar error it is indeed a fortran library missing.

[baj12]

quantreg is working:

install.packages("quantreg",type = "source")

.... MANY warnings ....

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: 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'
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-quantreg/00new/quantreg/libs
** R
** data
** demo
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

• DONE (quantreg)

The downloaded source packages are in
‘/private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/RtmpPCQjeV/downloaded_packages’

[Cortalak]

Alright it still seems to me that it is still the fortran library causing the problem. I'm currently trying to test on 4.0.2 on ubuntu machine I will keep you updated. Thanks for the feedback.

[Cortalak]

I have tested on both ubuntu 18.04 and windows10 and works fine on a freshly installed R 4.0.2 instance. Unfortunately I don't have a MAC system at hand right now. Moreover it seems that the link I sent got every dmg for recent MACOS apart from 10.13 High Sierra and that many user are encountering problem regarding GCC on MAC 10.13 regardless of the programming language. Still I'm convinced there must be a workaround using symbolic link and GCC compiler of other MAC OS version. Won't be soon but I will try to test these behavior on a hackintosh.

[baj12]

I can confirm, on Windows the installation is working. Not sure what is going on with my two Macs...
B