Failing to install Rhdf5lib: 'cannot find -lldap' and 'cannot find -llber'

[yentlprojects]

On a linux server I installed BiocManager to a specific R_LIBS directory and am now trying to install the flowCore library. I am using R version 4.0.2 and Bioconductor version 3.12.

Initally I did this using
Rscript -e "BiocManager::install('flowCore')"

This resulted in errors for flowCore not finding cytolib, which in turn couldn't find Rhdf5lib, due to errors with finding -lldap and -llber. Next I tried to install Rhdf5lib specifically using:
Rscript -e "BiocManager::install('grimbough/Rhdf5lib')"
and
Rscript -e "BiocManager::install('grimbough/Rhdf5lib', INSTALL_opts = '--force-biarch')"

which both resulted in the same output (can provide full log if needed):

  CC       H5HLdblk.lo
  CC       H5HP.lo
  CC       H5I.lo
  CC       H5Itest.lo
  CC       H5L.lo
  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
/apps/leuven/skylake/2018a/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: cannot find -lldap
/apps/leuven/skylake/2018a/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: cannot find -llber
collect2: error: ld returned 1 exit status
make[2]: *** [H5make_libsettings] Error 1
make[2]: Leaving directory `/tmp/RtmpWh6BJm/R.INSTALL10401ea40216/Rhdf5lib/src/hdf5/src'
make[1]: *** [lib] Error 1
make[1]: Leaving directory `/tmp/RtmpWh6BJm/R.INSTALL10401ea40216/Rhdf5lib/src/hdf5/src'
make: *** [lib] Error 1
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_HL_INCLUDE=hdf5/hl/src
configure:    HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure:    HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"libhdf5.settings "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: cannot stat 'hdf5/src/.libs/libhdf5.a': No such file or directory
make: *** [copying] Error 1
ERROR: compilation failed for package 'Rhdf5lib'
* removing '/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/Rhdf5lib'
Error: Failed to install 'Rhdf5lib' from GitHub:
  (converted from warning) installation of package '/tmp/RtmpYhjnOU/filec777dc6cd74/Rhdf5lib_1.11.3.tar.gz' had non-zero exit status
Execution halted
✘ [Dec/05 17:22] vsc32884@tier2-p-login-1 ~ $   CC       H5HLdbg.lo
  CC       H5HLint.lo
  CC       H5HLprfx.lo
  CC       H5HLdblk.lo
  CC       H5HP.lo
  CC       H5I.lo
  CC       H5Itest.lo
  CC       H5L.lo
  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
/apps/leuven/skylake/2018a/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: cannot find -lldap
/apps/leuven/skylake/2018a/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold: error: cannot find -llber
collect2: error: ld returned 1 exit status
make[2]: *** [H5make_libsettings] Error 1
make[2]: Leaving directory `/tmp/RtmpWh6BJm/R.INSTALL10401ea40216/Rhdf5lib/src/hdf5/src'
make[1]: *** [lib] Error 1
make[1]: Leaving directory `/tmp/RtmpWh6BJm/R.INSTALL10401ea40216/Rhdf5lib/src/hdf5/src'
make: *** [lib] Error 1
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_HL_INCLUDE=hdf5/hl/src
-bash: CC: command not foundc
onfigure:    HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure:    HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"libhdf5.settings "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: cannot stat 'hdf5/src/.libs/libhdf5.a': No such file or directory
make: *** [copying] Error 1
ERROR: compilation failed for package 'Rhdf5lib'
* removing '/vsc-hard-mounts/leuven-user/328/vsc32884/Rlibs/Rhdf5lib'
Error: Failed to install 'Rhdf5lib' from GitHub:
  (converted from warning) installation of package '/tmp/RtmpYhjnOU/filec777dc6cd74/Rhdf5lib_1.11.3.tar.gz' had non-zero exit status
Execution halted

Is this a known issue/is there a known fix for this? Or maybe an implicit dependency that is missing?

[grimbough]

I've never seen this issue before, and I can't find anything in the HDF5 documentation that refers to those libraries. I presume installing libldap and liblber would be sufficient to solve the issue, but that doesn't help understanding why it's a problem in the first place. I don't know why it would be picking them up from, but they are installed on my test system, so perhaps it's being used implicitly as you say.

Can you give the output from running R CMD config LDFLAGS and R CMD config CPPFLAGS in a terminal?

There's also a section of the package installation that falls between the two lines below which would be useful to see.

SUMMARY OF THE HDF5 CONFIGURATION
=================================
...
<Lots of compilation settings>
...
Features:
---------

[yentlprojects]

Thanks for your fast reply.

Hereby the results of the commands you mentioned:

R CMD config LDFLAGS

-L/apps/leuven/skylake/2018a/software/GCCcore/6.4.0/lib64 -L/apps/leuven/skylake/2018a/software/GCCcore/6.4.0/lib -L/apps/leuven/skylake/2018a/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib -L/apps/leuven/skylake/2018a/software/FFTW/3.3.7-gompi-2018a/lib -L/apps/leuven/skylake/2018a/software/libreadline/7.0-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/ncurses/6.0-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/libpng/1.6.34-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/Java/1.8.0_162/lib -L/apps/leuven/skylake/2018a/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/lib -L/apps/leuven/skylake/2018a/software/bzip2/1.0.6-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/cURL/7.58.0-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/PCRE2/10.21-foss-2018a/lib

R CMD config CPPFLAGS

-I/apps/leuven/skylake/2018a/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/apps/leuven/skylake/2018a/software/FFTW/3.3.7-gompi-2018a/include -I/apps/leuven/skylake/2018a/software/libreadline/7.0-GCCcore-6.4.0/include -I/apps/leuven/skylake/2018a/software/ncurses/6.0-GCCcore-6.4.0/include -I/apps/leuven/skylake/2018a/software/libpng/1.6.34-GCCcore-6.4.0/include -I/apps/leuven/skylake/2018a/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/apps/leuven/skylake/2018a/software/Java/1.8.0_162/include -I/apps/leuven/skylake/2018a/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/apps/leuven/skylake/2018a/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/apps/leuven/skylake/2018a/software/cURL/7.58.0-GCCcore-6.4.0/include -I/apps/leuven/skylake/2018a/software/PCRE2/10.21-foss-2018a/include

And also ran the installation again:

           SUMMARY OF THE HDF5 CONFIGURATION
            =================================

General Information:
-------------------
                   HDF5 Version: 1.10.6
                  Configured on: Mon Dec  7 20:06:11 CET 2020
                  Configured by: vsc32884@tier2-p-login-1
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux tier2-p-login-1 3.10.0-1127.18.2.el7.x86_64 #1 SMP Sun Jul 26 15:27:06 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /tmp/RtmpqE2lRz/R.INSTALL41034aeb094/Rhdf5lib/src/hdf5/hdf5

Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high

Linking Options:
----------------
                      Libraries: static
  Statically Linked Executables:
                        LDFLAGS: -L/apps/leuven/skylake/2018a/software/GCCcore/6.4.0/lib64 -L/apps/leuven/skylake/2018a/software/GCCcore/6.4.0/lib -L/apps/leuven/skylake/2018a/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib -L/apps/leuven/skylake/2018a/software/FFTW/3.3.7-gompi-2018a/lib -L/apps/leuven/skylake/2018a/software/libreadline/7.0-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/ncurses/6.0-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/libpng/1.6.34-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/Java/1.8.0_162/lib -L/apps/leuven/skylake/2018a/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/lib -L/apps/leuven/skylake/2018a/software/bzip2/1.0.6-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/cURL/7.58.0-GCCcore-6.4.0/lib -L/apps/leuven/skylake/2018a/software/PCRE2/10.21-foss-2018a/lib
                     H5_LDFLAGS:
                     AM_LDFLAGS:  -L/tmp/RtmpqE2lRz/R.INSTALL41034aeb094/Rhdf5lib/src/hdf5/szip/szip/lib
                Extra libraries: -lcrypto -lcurl -lsz -lz -ldl -lm
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /apps/leuven/skylake/2018a/software/GCCcore/6.4.0/bin/gcc ( gcc (GCC) 6.4.0)
                       CPPFLAGS:
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/tmp/RtmpqE2lRz/R.INSTALL41034aeb094/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -O2 -march=native -w -fpic
                     H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wnull-dereference -Wunused-const-variable -Wduplicated-cond -Whsa -Wnormalized -fstdarg-opt -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -O3
                     AM C Flags:
               Shared C Library: no
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /apps/leuven/skylake/2018a/software/GCCcore/6.4.0/bin/g++ -std=gnu++11 ( g++ (GCC) 6.4.0)
                      C++ Flags: -O2 -march=native -w -fpic
                   H5 C++ Flags: -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wendif-labels -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -Wdate-time -Wopenmp-simd -Warray-bounds=2 -fstdarg-opt -s -O3
                   AM C++ Flags:
             Shared C++ Library: no
             Static C++ Library: yes

                           Java: no


Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                Build HDF5 Tests: yes
                Build HDF5 Tools: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                      Direct VFD: no
              (Read-Only) S3 VFD: yes
            (Read-Only) HDFS VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
          Function stack tracing: no
       Strict file format checks: no
    Optimization instrumentation: no

Thanks in advance for your assistance.

[grimbough]

Thanks for that. I notice that the CPPFLAGS are not being passed to the installer, so I've changed that. You can try testing via:

BiocManager::install("grimbough/Rhdf5lib", ref = "cpp-flags")

I don't think that's going to be the solution though, as that should address finding header files rather than libraries. There's nothing obvious in the output that refers to libldap or libber, so presumably they're actually referenced by one of the other libraries. My guess would be libcurl, you can install a version of Rhdf5lib that doesn't use curl with:

BiocManager::install('grimbough/Rhdf5lib', ref="cpp-flags", configure.args = "--disable-ros3-vfd")

If that's still not working it might be good to run locate libldap and ldconfig -p | grep ldap to try and get an understanding of where that library is on your system.

[yentlprojects]

The first solution you proposed actually did the trick it seems. Managed to install Rhdf5lib (and flowCore) and get my scripts running!

Thanks a lot!

[grimbough]

Great, that was definitely an oversight in the installation process and needed to be fixed, but I wasn't expecting it to work here! Glad it is. I'll merge the change into the devel and release versions of the package in Bioconductor, so you should be able to install using the standard mechanism going forward.

[grimbough]

This patch should now be in both release (>= 1.12.1) and devel (>= 1.13.2). Please reopen the issue if you encounter it again.

[ColeWunderlich]

I am also getting the same error on CentOS 8 with R 4.0.2 and GCC 8.3.0

Looks like it is related to the gold linker and GCC.

Abbreviated output below (full dump attached)

	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
                   HDF5 Version: 1.10.6
                  Configured on: Tue Feb 23 00:21:49 EST 2021
                  Configured by: wunderl@bamdev1
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux bamdev1 4.18.0-193.14.2.el8_2.x86_64 #1 SMP Sun Jul 26 03:54:29 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /tmp/Rtmp0PHxII/R.INSTALL3d4e859dace7c/Rhdf5lib/src/hdf5/hdf5

Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high

Linking Options:
----------------
                      Libraries: static
  Statically Linked Executables: 
                        LDFLAGS: -L/grid/it/data/elzar/easybuild/software/GLPK/4.65-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/ImageMagick/7.0.9-5-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/GSL/2.6-GCC-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/UDUNITS/2.2.26-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/HDF5/1.10.5-gompi-2019b/lib -L/grid/it/data/elzar/easybuild/software/ICU/64.2-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/libsndfile/1.0.28-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/FFTW/3.3.8-gompi-2019b/lib -L/grid/it/data/elzar/easybuild/software/NLopt/2.6.1-GCCcore-8.3.0/lib64 -L/grid/it/data/elzar/easybuild/software/GMP/6.1.2-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/libxml2/2.9.9-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/cURL/7.66.0-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/Tk/8.6.9-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/Java/11.0.2/lib -L/grid/it/data/elzar/easybuild/software/LibTIFF/4.0.10-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/libjpeg-turbo/2.0.3-GCCcore-8.3.0/lib64 -L/grid/it/data/elzar/easybuild/software/libpng/1.6.37-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/PCRE/8.43-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/SQLite/3.29.0-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/zlib/1.2.11-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/XZ/5.2.4-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/bzip2/1.0.8-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/ncurses/6.1-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/libreadline/8.0-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/cairo/1.16.0-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/libGLU/9.0.1-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/Mesa/19.1.7-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/X11/20190717-GCCcore-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/ScaLAPACK/2.0.2-gompi-2019b/lib -L/grid/it/data/elzar/easybuild/software/OpenBLAS/0.3.7-GCC-8.3.0/lib -L/grid/it/data/elzar/easybuild/software/GCCcore/8.3.0/lib64 -L/grid/it/data/elzar/easybuild/software/GCCcore/8.3.0/lib
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/tmp/Rtmp0PHxII/R.INSTALL3d4e859dace7c/Rhdf5lib/src/hdf5/szip/szip/lib
                Extra libraries: -lcrypto -lcurl -lsz -lz -ldl -lm 
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /grid/it/data/elzar/easybuild/software/GCCcore/8.3.0/bin/gcc ( gcc (GCC) 8.3.0)
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/tmp/Rtmp0PHxII/R.INSTALL3d4e859dace7c/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -O2 -ftree-vectorize -march=native -fno-math-errno -w -fpic
                     H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wnull-dereference -Wunused-const-variable -Wduplicated-cond -Whsa -Wnormalized -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=2 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -fstdarg-opt -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
                     AM C Flags: 
               Shared C Library: no
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /grid/it/data/elzar/easybuild/software/GCCcore/8.3.0/bin/g++ -std=gnu++11 ( g++ (GCC) 8.3.0)
                      C++ Flags: -O2 -ftree-vectorize -march=native -fno-math-errno -w -fpic
                   H5 C++ Flags:   -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
                   AM C++ Flags: 
             Shared C++ Library: no
             Static C++ Library: yes

                           Java: no


Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                Build HDF5 Tests: yes
                Build HDF5 Tools: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                      Direct VFD: no
              (Read-Only) S3 VFD: yes
            (Read-Only) HDFS VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
          Function stack tracing: no
       Strict file format checks: no
    Optimization instrumentation: no
for d in src . c++ hl; do                                \
  if test $d != .; then                                        \
   (cd $d && make  lib) || exit 1;            \
  fi;                                                           \
done
make[1]: Entering directory '/tmp/Rtmp0PHxII/R.INSTALL3d4e859dace7c/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/tmp/Rtmp0PHxII/R.INSTALL3d4e859dace7c/Rhdf5lib/src/hdf5/src'
..........
  CC       H5Itest.lo
  CC       H5L.lo
  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
/grid/it/data/elzar/easybuild/software/binutils/2.32-GCCcore-8.3.0/bin/ld.gold: error: cannot find -lldap
/grid/it/data/elzar/easybuild/software/binutils/2.32-GCCcore-8.3.0/bin/ld.gold: error: cannot find -llber
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1122: H5make_libsettings] Error 1
make[2]: Leaving directory '/tmp/Rtmp0PHxII/R.INSTALL3d4e859dace7c/Rhdf5lib/src/hdf5/src'
make[1]: *** [Makefile:1989: lib] Error 1
make[1]: Leaving directory '/tmp/Rtmp0PHxII/R.INSTALL3d4e859dace7c/Rhdf5lib/src/hdf5/src'
make: *** [Makefile:1088: lib] Error 1
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_HL_INCLUDE=hdf5/hl/src
configure:    HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure:    HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/grid/wsbs/home_norepl/wunderl/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/grid/wsbs/home_norepl/wunderl/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/grid/wsbs/home_norepl/wunderl/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/grid/wsbs/home_norepl/wunderl/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/grid/wsbs/home_norepl/wunderl/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/grid/wsbs/home_norepl/wunderl/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/grid/wsbs/home_norepl/wunderl/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: cannot stat 'hdf5/src/.libs/libhdf5.a': No such file or directory
make: *** [Makevars:38: copying] Error 1
ERROR: compilation failed for package ‘Rhdf5lib’

hdf5lib_errorDump.txt

[ColeWunderlich]

Update: I just realized the latest version available through Bioconductor for R 4.0.2 is Rhdf5lib 1.12.1 which does not contain the patch mentioned here.

Installing from github@master failed as it requires R>4.1.0. Installing from github@cpp-flags , however, worked!

I don't know if it's possible, but it would be nice to update the package on Bioconductor 3.12 to include the cpp-flags patch, as it appears the current v1.12.1 lacks the patch causing it to break on CentOS.

[grimbough]

Thanks for the extra info. I thought I'd merged that cpp-flag patch into the release version, but perhaps not. I thought that the issue was not passing CPP_FLAGS during compilation, but I see them in the build reports for 1.12.1 e.g. CPPFLAGS: -I/usr/local/include in http://bioconductor.org/checkResults/release/bioc-LATEST/Rhdf5lib/nebbiolo1-install.html

Does it also fail if you installed the RELEASE_3_12 branch from here?

BiocManager::install("grimbough/Rhdf5lib", ref = "RELEASE_3_12")

That should be identical to the Bioconductor 3.12 version (assuming I've pushed to all the correct places). Maybe also confirm you're definitely using Bioconductor 3.12 with BiocManager::version() ?

[ColeWunderlich]

With respect to the build report, it looks like fundamentally different code is being run, perhaps a shell script designed to handle this exception that is not currently included in 1.12.1.

The relevant bit from the build report

  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/lib |                  \
	sed -e 's/-L/:/g' -e 's/ //g'`"                               \
 ./H5make_libsettings > H5lib_settings.c  ||                               \
    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
    (rm -f H5lib_settings.c ; exit 1)
  CC       H5lib_settings.lo

But on my system

  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
/grid/it/data/elzar/easybuild/software/binutils/2.32-GCCcore-8.3.0/bin/ld.gold: error: cannot find -lldap
/grid/it/data/elzar/easybuild/software/binutils/2.32-GCCcore-8.3.0/bin/ld.gold: error: cannot find -llber
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1122: H5make_libsettings] Error 1

It is also true, however, that my system does not have the cpp flags listed and they are listed in the build report.

As for the other questions:

• RELEASE_3_12 gives me the same error but does show the cpp flags

Languages:
----------
                              C: yes
                     C Compiler: /grid/it/data/elzar/easybuild/software/GCCcore/8.3.0/bin/gcc ( gcc (GCC) 8.3.0)
                       CPPFLAGS: -I/grid/it/data/elzar/easybuild/software/GLPK/4.65-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/ImageMagick/7.0.9-5-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/GSL/2.6-GCC-8.3.0/include -I/grid/it/data/elzar/easybuild/software/UDUNITS/2.2.26-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/HDF5/1.10.5-gompi-2019b/include -I/grid/it/data/elzar/easybuild/software/ICU/64.2-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/libsndfile/1.0.28-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/FFTW/3.3.8-gompi-2019b/include -I/grid/it/data/elzar/easybuild/software/NLopt/2.6.1-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/GMP/6.1.2-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/libxml2/2.9.9-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/cURL/7.66.0-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/Tk/8.6.9-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/Java/11.0.2/include -I/grid/it/data/elzar/easybuild/software/LibTIFF/4.0.10-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/libjpeg-turbo/2.0.3-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/libpng/1.6.37-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/PCRE/8.43-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/SQLite/3.29.0-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/zlib/1.2.11-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/XZ/5.2.4-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/bzip2/1.0.8-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/ncurses/6.1-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/libreadline/8.0-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/cairo/1.16.0-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/libGLU/9.0.1-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/Mesa/19.1.7-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/X11/20190717-GCCcore-8.3.0/include -I/grid/it/data/elzar/easybuild/software/ScaLAPACK/2.0.2-gompi-2019b/include -I/grid/it/data/elzar/easybuild/software/OpenBLAS/0.3.7-GCC-8.3.0/include
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/tmp/Rtmpe9Oa5d/R.INSTALL191f7d594de3d4/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -O2 -ftree-vectorize -march=native -fno-math-errno -w -fpic
                     H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wnull-dereference -Wunused-const-variable -Wduplicated-cond -Whsa -Wnormalized -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=2 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -fstdarg-opt -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
                     AM C Flags: 
               Shared C Library: no
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /grid/it/data/elzar/easybuild/software/GCCcore/8.3.0/bin/g++ -std=gnu++11 ( g++ (GCC) 8.3.0)
                      C++ Flags: -O2 -ftree-vectorize -march=native -fno-math-errno -w -fpic
                   H5 C++ Flags:   -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
                   AM C++ Flags: 
             Shared C++ Library: no
             Static C++ Library: yes

                           Java: no

#later
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
/grid/it/data/elzar/easybuild/software/binutils/2.32-GCCcore-8.3.0/bin/ld.gold: error: cannot find -lldap
/grid/it/data/elzar/easybuild/software/binutils/2.32-GCCcore-8.3.0/bin/ld.gold: error: cannot find -llber
collect2: error: ld returned 1 exit status

• Apparently I am actually on Bioconductor version 3.11 as 3.12 is only supported for R 4.0.3 and up.
• Downloading the v1.12.1 tarball from Bioc 13.12 and installing from source yields the same error. The 1.12.1 install does show the cpp flags, however, and looks the same as the output from RELEASE_3_12
• Installing v1.10.1 from Bioc 3.11 also yields the same error

Overall it looks like it is not actually the missing CPPFLAGS that is causing the error, but rather something the cpp-flags branch has that RELEASE_3_12 lacks. Comparing the two branches on github, however, I do see a few places RELEASE_3_12 lacks the cpp flags.

In this diff lines 2158, 3890, and 3903 in configure are missing CPPFLAGS. Lines 23, 116, and 129 in configure.ac are also missing the flags.

[grimbough]

Thanks for the detective work. I think what must have happened is that I merged the cpp-branch into the Bioconductor devel branch, but then just tried to apply the changes manually to RELEASE_3_12. I guess I didn't do that successfully! I'll apply the missing parts to the branch and create version 1.12.2.

I'm only able to do this for 3.12. The 3.11 branch is locked now at Bioconductor, so I'm afraid that will never be patched.

---

Also, despite what it says at https://www.bioconductor.org/news/bioc_3_12_release/ about being tied to R-4.0.3 I think you should be fine to use any version of R-4.0.Z. AFAIK Bioconductor versions are tied to the Y parts of R-X.Y.Z, but not the point releases.