Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Installation problem #13

Open
michelem99 opened this issue Nov 21, 2024 · 3 comments
Open

Installation problem #13

michelem99 opened this issue Nov 21, 2024 · 3 comments

Comments

@michelem99
Copy link

michelem99 commented Nov 21, 2024 •
edited
Loading

I tried to install "RcppPlanc" with: install.packages("RcppPlanc", repos = "https://welch-lab.r-universe.dev"), but the output shows an error. It seems there might be an issue with the "hdf5" library, although it's already installed.
Could someone help me?

> > install.packages("RcppPlanc", repos = "https://welch-lab.r-universe.dev")
Installing package into ‘/srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://welch-lab.r-universe.dev/src/contrib/RcppPlanc_1.0.0.tar.gz'
Content type 'application/gzip' length 1426070 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘RcppPlanc’ ...
** using staged installation
-- The C compiler identification is GNU 8.5.0
-- The CXX compiler identification is GNU 8.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  R not found (missing: R_EXECUTABLE)
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
  cmake/FindR.cmake:120 (find_package_handle_standard_args)
  CMakeLists.txt:30 (find_package)


-- Configuring incomplete, errors occurred!
./configure: line 46: _deps/highfive-src/include/highfive/bits/H5Friends.hpp: No such file or directory
ERROR: configuration failed for package ‘RcppPlanc’
* removing ‘/srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/RcppPlanc’
Warning in install.packages :
  installation of package ‘RcppPlanc’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpzgO9Mz/downloaded_packages’
@theAeon
Copy link
Member

theAeon commented Nov 21, 2024

Is R on your path?

@michelem99
Copy link
Author

Hi, thanks for the reply.
I am using Rstudio server and for some strange reasons R was not in the path.
Now after I added it, I get a different error:


── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/Rtmpnli7Bh/remotesba04179edb8e/welch-lab-RcppPlanc-4f705f9/DESCRIPTION’ ...
─  preparing ‘RcppPlanc’:
✔  checking DESCRIPTION meta-information
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘RcppPlanc_1.0.0.tar.gz’
   
Installing package into ‘/srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘RcppPlanc’ ...
** using staged installation
-- The C compiler identification is GNU 8.5.0
-- The CXX compiler identification is GNU 8.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found R: /opt/R/4.4.2/bin/R (found version "4.4.2") 
-- MKL_THREADING = OMP
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of void*
-- Check size of void* - done
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib64/libopenblas.so  
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib64/libopenblas.so;-lpthread;-lm;-ldl  
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Found R_Rcpp: /srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/Rcpp  
-- Found R_RcppArmadillo: /srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/RcppArmadillo  
-- Found R_RcppProgress: /srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/RcppProgress  
-- A cache variable, namely HWLOC_DIR, has been set to specify the install directory of HWLOC
-- Checking for one of the modules 'hwloc'
-- Looking for HWLOC - not found using PkgConfig.
   Perhaps you should add the directory containing hwloc.pc to
   the PKG_CONFIG_PATH environment variable.
-- Looking for HWLOC - PkgConfig not used
-- Looking for hwloc -- hwloc.h not found
-- Looking for hwloc -- lib hwloc not found
-- Could NOT find HWLOC (missing: HWLOC_LIBRARIES HWLOC_WORKS) 
CMake Warning (dev) at /usr/share/cmake/Modules/ExternalProject.cmake:3091 (message):
  The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is
  not set.  The policy's OLD behavior will be used.  When using a URL
  download, the timestamps of extracted files should preferably be that of
  the time of extraction, otherwise code that depends on the extracted
  contents might not be rebuilt if the URL changes.  The OLD behavior
  preserves the timestamps from the archive instead, but this is usually not
  what you want.  Update your project to the NEW behavior or specify the
  DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this
  robustness issue.
Call Stack (most recent call first):
  /usr/share/cmake/Modules/ExternalProject.cmake:4208 (_ep_add_download_command)
  CMakeLists.txt:141 (ExternalProject_Add)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /usr/share/cmake/Modules/FetchContent.cmake:1282 (message):
  The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is
  not set.  The policy's OLD behavior will be used.  When using a URL
  download, the timestamps of extracted files should preferably be that of
  the time of extraction, otherwise code that depends on the extracted
  contents might not be rebuilt if the URL changes.  The OLD behavior
  preserves the timestamps from the archive instead, but this is usually not
  what you want.  Update your project to the NEW behavior or specify the
  DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this
  robustness issue.
Call Stack (most recent call first):
  CMakeLists.txt:168 (FetchContent_Declare)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
-- Found HDF5: /usr/lib64/libhdf5.so (found version "1.10.5")  
-- Looking for std::filesystem::exists
-- Looking for std::filesystem::exists - not found
-- Performing Test FINITE_MATH
-- Performing Test FINITE_MATH - Success
-- Performing Test SIGNALING_NANS
-- Performing Test SIGNALING_NANS - Success
-- Performing Test ROUNDING_MATH
-- Performing Test ROUNDING_MATH - Success
-- Performing Test TRAPPING_MATH
-- Performing Test TRAPPING_MATH - Success
-- Performing Test ERRNO_MATH
-- Performing Test ERRNO_MATH - Success
-- Performing Test UNSIGNED_ZERO
-- Performing Test UNSIGNED_ZERO - Success
-- Looking for openblas/cblas.h
-- Looking for openblas/cblas.h - found
-- Configuring done (6.2s)
-- Generating done (0.0s)
-- Build files have been written to: /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src
** libs
/usr/bin/cmake -S/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools -B/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/CMakeFiles /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
make  -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/depend
make[2]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/CMakeFiles/hwloc.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
make  -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/build
make[2]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
[  7%] Creating directories for 'hwloc'
/usr/bin/cmake -Dcfgdir= -P /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/tmp/hwloc-mkdirs.cmake
/usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-mkdir
[ 14%] Performing download step (download, verify and extract) for 'hwloc'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src && /usr/bin/cmake -P /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/download-hwloc.cmake
-- Downloading...
   dst='/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-2.9.3.tar.gz'
   timeout='none'
   inactivity timeout='none'
-- Using src='https://download.open-mpi.org/release/hwloc/v2.9/hwloc-2.9.3.tar.gz'
-- [download 0% complete]
-- [download 1% complete]
-- [download 2% complete]
-- [download 3% complete]
-- [download 4% complete]
-- [download 5% complete]
-- [download 6% complete]
-- [download 7% complete]
-- [download 8% complete]
-- [download 9% complete]
-- [download 10% complete]
-- [download 11% complete]
-- [download 12% complete]
-- [download 13% complete]
-- [download 14% complete]
-- [download 15% complete]
-- [download 16% complete]
-- [download 17% complete]
-- [download 18% complete]
-- [download 19% complete]
-- [download 20% complete]
-- [download 21% complete]
-- [download 22% complete]
-- [download 23% complete]
-- [download 24% complete]
-- [download 25% complete]
-- [download 26% complete]
-- [download 27% complete]
-- [download 28% complete]
-- [download 29% complete]
-- [download 30% complete]
-- [download 31% complete]
-- [download 32% complete]
-- [download 33% complete]
-- [download 34% complete]
-- [download 35% complete]
-- [download 36% complete]
-- [download 37% complete]
-- [download 38% complete]
-- [download 39% complete]
-- [download 40% complete]
-- [download 41% complete]
-- [download 42% complete]
-- [download 43% complete]
-- [download 44% complete]
-- [download 45% complete]
-- [download 46% complete]
-- [download 47% complete]
-- [download 48% complete]
-- [download 49% complete]
-- [download 50% complete]
-- [download 51% complete]
-- [download 52% complete]
-- [download 53% complete]
-- [download 54% complete]
-- [download 55% complete]
-- [download 56% complete]
-- [download 57% complete]
-- [download 58% complete]
-- [download 59% complete]
-- [download 60% complete]
-- [download 61% complete]
-- [download 62% complete]
-- [download 63% complete]
-- [download 64% complete]
-- [download 65% complete]
-- [download 66% complete]
-- [download 67% complete]
-- [download 68% complete]
-- [download 69% complete]
-- [download 70% complete]
-- [download 71% complete]
-- [download 72% complete]
-- [download 73% complete]
-- [download 74% complete]
-- [download 75% complete]
-- [download 76% complete]
-- [download 77% complete]
-- [download 78% complete]
-- [download 79% complete]
-- [download 80% complete]
-- [download 81% complete]
-- [download 82% complete]
-- [download 83% complete]
-- [download 84% complete]
-- [download 85% complete]
-- [download 86% complete]
-- [download 87% complete]
-- [download 88% complete]
-- [download 89% complete]
-- [download 90% complete]
-- [download 91% complete]
-- [download 92% complete]
-- [download 93% complete]
-- [download 94% complete]
-- [download 95% complete]
-- [download 96% complete]
-- [download 97% complete]
-- [download 98% complete]
-- [download 99% complete]
-- [download 100% complete]
-- verifying file...
       file='/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-2.9.3.tar.gz'
-- Downloading... done
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src && /usr/bin/cmake -P /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/verify-hwloc.cmake
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src && /usr/bin/cmake -P /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/extract-hwloc.cmake
-- extracting...
     src='/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-2.9.3.tar.gz'
     dst='/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src && /usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-download
[ 21%] No update step for 'hwloc'
/usr/bin/cmake -E echo_append
/usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-update
[ 28%] Performing patch step for 'hwloc'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc && /usr/bin/cmake -E cat /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/patches/00_remove_stdio.patch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/patches/01_remove_sprintf.patch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/patches/02_adjust_windows_types.patch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/patches/03_remove_abort.patch | /usr/bin/patch -p1 -l
patching file hwloc/components.c
patching file hwloc/distances.c
patching file hwloc/memattrs.c
patching file hwloc/pci-common.c
patching file hwloc/topology-aix.c
patching file hwloc/topology-bgq.c
patching file hwloc/topology-cuda.c
patching file hwloc/topology-darwin.c
patching file hwloc/topology-levelzero.c
patching file hwloc/topology-linux.c
patching file hwloc/topology-nvml.c
patching file hwloc/topology-opencl.c
patching file hwloc/topology-pci.c
patching file hwloc/topology-rsmi.c
patching file hwloc/topology-solaris.c
patching file hwloc/topology-synthetic.c
patching file hwloc/topology-windows.c
patching file hwloc/topology-x86.c
patching file hwloc/topology-xml-libxml.c
patching file hwloc/topology-xml-nolibxml.c
patching file hwloc/topology-xml.c
patching file hwloc/topology.c
patching file hwloc/cpukinds.c
patching file hwloc/topology-freebsd.c
patching file hwloc/topology-linux.c
patching file hwloc/topology-rsmi.c
patching file hwloc/topology-windows.c
patching file hwloc/topology-xml.c
patching file include/hwloc/cuda.h
patching file include/hwloc/cudart.h
patching file include/hwloc/levelzero.h
patching file include/hwloc/nvml.h
patching file include/hwloc/opencl.h
patching file include/hwloc/openfabrics-verbs.h
patching file include/hwloc/rsmi.h
patching file hwloc/topology-windows.c
patching file hwloc/distances.c
patching file hwloc/topology-linux.c
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc && /usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-patch
[ 35%] Performing configure step for 'hwloc'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E env LD=ld "CFLAGS=-DNDEBUG -I/usr/local/include -g -O2  " sh ../hwloc/configure --with-pic --prefix=/out/ --disable-picky --enable-shared=no --enable-static=yes --disable-cairo --disable-libxml2 --disable-io --disable-plugin-dlopen --disable-plugin-ltdl --enable-embedded-mode

###
### Configuring hwloc distribution tarball
### Startup tests
###
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1105' is supported by ustar format... yes
checking whether GID '1105' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for wchar.h... yes
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
checking for ar... ar
checking the archiver (ar) interface... ar
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... ld
checking if the linker (ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... ld -m elf_x86_64
checking if the linker (ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking for gcc options needed to detect all undeclared functions... none needed
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking how to run the C preprocessor... gcc -E
checking for X... libraries , headers 

###
### Configuring hwloc core
###
checking hwloc building mode... embedded
configure: hwloc builddir: /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build
configure: hwloc srcdir: /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc
configure: Detected VPATH build
checking for hwloc version... 2.9.3
checking if want hwloc maintainer support... disabled (embedded mode)
checking for hwloc directory prefix... (none)
checking for hwloc symbol prefix... hwloc_
checking for the C compiler vendor... gnu
checking size of void *... 8
checking which OS support to include... Linux
checking which CPU support to include... x86_64
checking size of unsigned long... 8
checking size of unsigned int... 4
checking for __attribute__... yes
checking for __attribute__(aligned)... yes
checking for __attribute__(always_inline)... yes
checking for __attribute__(cold)... yes
checking for __attribute__(const)... yes
checking for __attribute__(deprecated)... yes
checking for __attribute__(constructor)... yes
checking for __attribute__(format)... yes
checking for __attribute__(hot)... yes
checking for __attribute__(malloc)... yes
checking for __attribute__(may_alias)... yes
checking for __attribute__(no_instrument_function)... yes
checking for __attribute__(nonnull)... yes
checking for __attribute__(noreturn)... yes
checking for __attribute__(packed)... yes
checking for __attribute__(pure)... yes
checking for __attribute__(sentinel)... yes
checking for __attribute__(unused)... yes
checking for __attribute__(warn_unused_result)... yes
checking for __attribute__(weak_alias)... yes
checking if gcc supports -fvisibility=hidden... yes
checking whether to enable symbol visibility... yes (via -fvisibility=hidden)
configure: WARNING: "-fvisibility=hidden" has been added to the hwloc CFLAGS
checking whether the C compiler rejects function calls with too many arguments... yes
checking whether the C compiler rejects function calls with too few arguments... yes
checking for unistd.h... (cached) yes
checking for dirent.h... yes
checking for strings.h... (cached) yes
checking for ctype.h... yes
checking for strcasecmp... yes
checking whether strcasecmp is declared... yes
checking whether function strcasecmp has a complete prototype... yes
checking for strncasecmp... yes
checking whether strncasecmp is declared... yes
checking whether function strncasecmp has a complete prototype... yes
checking for strftime... yes
checking for setlocale... yes
checking for stdint.h... (cached) yes
checking for sys/mman.h... yes

**** Linux-specific checks
checking whether sched_getcpu is declared... yes
checking whether sched_setaffinity is declared... yes
checking whether function sched_setaffinity has a complete prototype... yes
checking for old prototype of sched_setaffinity... no
checking for working CPU_SET... yes
checking for working CPU_SET_S... yes
checking for working syscall with 6 parameters... yes
checking for libudev.h... no
**** end of Linux-specific checks

checking whether pthread_setaffinity_np is declared... yes
checking whether pthread_getaffinity_np is declared... yes
checking whether fabsf is declared... yes
checking for fabsf in -lm... yes
checking whether modff is declared... yes
checking for modff in -lm... yes
checking whether _SC_NPROCESSORS_ONLN is declared... yes
checking whether _SC_NPROCESSORS_CONF is declared... yes
checking whether _SC_NPROC_ONLN is declared... no
checking whether _SC_NPROC_CONF is declared... no
checking whether _SC_PAGESIZE is declared... yes
checking whether _SC_PAGE_SIZE is declared... yes
checking whether _SC_LARGE_PAGESIZE is declared... no
checking for mach/mach_init.h... no
checking for mach_init.h... no
checking for mach/mach_host.h... no
checking whether strtoull is declared... yes
checking for ssize_t... yes
checking whether snprintf is declared... yes
checking whether _strdup is declared... no
checking whether _putenv is declared... no
checking whether snprintf is correct... yes
checking whether getprogname is declared... no
checking whether getexecname is declared... no
checking for program_invocation_name... yes
checking for __progname... yes
checking for pthread_t... yes
checking for bash... /usr/bin/sh
checking for ffs... yes
checking whether ffs is declared... yes
checking whether function ffs has a complete prototype... yes
checking for ffsl... yes
checking whether ffsl is declared... yes
checking whether function ffsl has a complete prototype... yes
checking for fls... no
checking for flsl... no
checking for clz... no
checking for clzl... no
checking for openat... yes
checking for malloc.h... yes
checking for getpagesize... yes
checking for memalign... yes
checking for posix_memalign... yes
checking for sys/utsname.h... yes
checking for uname... yes
checking for pthread_mutex_lock... yes

**** x86 CPUID configuration
checking for x86 cpuid... yes
**** end of x86 CPUID configuration

**** component and plugin-specific configuration
checking if plugin support is enabled... no
checking components to build statically...  noos xml synthetic xml_nolibxml linux x86
checking components to build as plugins... 
**** end of component and plugin configuration
checking for diff... /usr/bin/diff

###
### Performing final hwloc configuration
###
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating include/Makefile
config.status: creating hwloc/Makefile
config.status: creating include/private/autogen/config.h
config.status: creating include/hwloc/autogen/config.h
config.status: executing depfiles commands
config.status: executing libtool commands

-----------------------------------------------------------------------------
Hwloc optional build support status (more details can be found above):

Probe / display I/O devices: no
Graphical output:            no (disabled in embedded mode)
XML input / output:          basic
Netloc functionality:        no
Plugin support:              no
-----------------------------------------------------------------------------

cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-configure
[ 42%] Performing build step for 'hwloc'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build && make
make[3]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
Making all in include
make[4]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include'
Making all in hwloc
make[4]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
  CC       topology.lo
  CC       traversal.lo
  CC       distances.lo
  CC       memattrs.lo
  CC       cpukinds.lo
  CC       components.lo
  CC       bind.lo
  CC       bitmap.lo
  CC       pci-common.lo
  CC       diff.lo
  CC       shmem.lo
  CC       misc.lo
  CC       base64.lo
  CC       topology-noos.lo
  CC       topology-synthetic.lo
  CC       topology-xml.lo
  CC       topology-xml-nolibxml.lo
  CC       topology-linux.lo
  CC       topology-hardwired.lo
  CC       topology-x86.lo
  CCLD     libhwloc_embedded.la
make[4]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
make[4]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
make[3]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-build
[ 50%] Performing install step for 'hwloc'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build && make install
make[3]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
Making install in include
make[4]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include'
make[5]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include'
make[5]: Nothing to be done for 'install-exec-am'.
make[5]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include'
make[4]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include'
Making install in hwloc
make[4]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
make[5]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
make  install-exec-hook
make[6]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
make[6]: Nothing to be done for 'install-exec-hook'.
make[6]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
make[5]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
make[4]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/hwloc'
make[4]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
make[5]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
make[5]: Nothing to be done for 'install-exec-am'.
make[5]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
make[4]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
make[3]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-install
[ 57%] Completed 'hwloc'
/usr/bin/cmake -E make_directory /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/CMakeFiles
/usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/CMakeFiles/hwloc-complete
/usr/bin/cmake -E touch /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-done
/usr/bin/cmake -E remove_directory /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc/utils/lstopo
make[2]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
[ 57%] Built target hwloc
make  -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/depend
make[2]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/CMakeFiles/hw_detect.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
make  -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/build
make[2]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
[ 64%] Building C object CMakeFiles/hw_detect.dir/common/hw_detect.c.o
/usr/bin/gcc  -I/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include -I/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/hwloc-prefix/src/hwloc/include -I/usr/local/include -g -O2 -O2 -g -DNDEBUG -std=gnu99 -fPIC -MD -MT CMakeFiles/hw_detect.dir/common/hw_detect.c.o -MF CMakeFiles/hw_detect.dir/common/hw_detect.c.o.d -o CMakeFiles/hw_detect.dir/common/hw_detect.c.o -c /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/common/hw_detect.c
make[2]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
[ 64%] Built target hw_detect
make  -f CMakeFiles/RcppPlanc.dir/build.make CMakeFiles/RcppPlanc.dir/depend
make[2]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
cd /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/CMakeFiles/RcppPlanc.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
make  -f CMakeFiles/RcppPlanc.dir/build.make CMakeFiles/RcppPlanc.dir/build
make[2]: Entering directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
[ 71%] Building CXX object CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o
/usr/bin/g++ -DHAVE_OPENBLAS_CBLAS_H -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -I/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/../src/common -I/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/../src/nnls -I/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/../src/nmf -I/opt/R/4.4.2/lib/R/include -I/srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include -I/srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/RcppArmadillo/include -I/srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/RcppProgress/include -I/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/_deps/highfive-src/include -I/usr/local/include -g -O2 -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -ffinite-math-only -fno-signaling-nans -fno-rounding-math -fno-trapping-math -fno-math-errno -fno-signed-zeros -MD -MT CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o -MF CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o.d -o CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o -c /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/rcppplanc_nmf.cpp
In file included from /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/../src/common/nmf.hpp:6,
                 from /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/../src/nmf/bppnmf.hpp:7,
                 from /tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src/rcppplanc_nmf.cpp:9:
/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/../src/common/utils.hpp: In function ‘void makeSparse(double, T*)’:
/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/tools/../src/common/utils.hpp:142:59: error: ‘sparsity’ is predetermined ‘shared’ for ‘shared’
 #pragma omp parallel for default(none) shared(sparsity, X)
                                                           ^
make[2]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
make[2]: *** [CMakeFiles/RcppPlanc.dir/build.make:79: CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:107: CMakeFiles/RcppPlanc.dir/all] Error 2
make[1]: Leaving directory '/tmp/RtmpFELAoh/R.INSTALLbf065f13ebb8/RcppPlanc/src'
make: *** [Makefile:139: all] Error 2
ERROR: compilation failed for package ‘RcppPlanc’
* removing ‘/srv/ngs/analysis/michele/R/x86_64-pc-linux-gnu-library/4.4/RcppPlanc’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmpnli7Bh/fileba0449e2458c/RcppPlanc_1.0.0.tar.gz’ had non-zero exit status

@theAeon
Copy link
Member

theAeon commented Nov 21, 2024

From the readme: OpenMP implementation that uses v4.0 semantics (if using OpenMP). For the GNU stack, this means gcc 9.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@theAeon @michelem99