Problem installing 'rhdf5': g++: error: [1]: No such file or directory
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Entering edit mode
rebeliscu • 0
@rebeliscu-19945
Last seen 11 days ago
United States

I'm having issues install rhdf5:


> BiocManager::install("rhdf5")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'rhdf5'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/rhdf5_2.38.0.tar.gz'
Content type 'application/x-gzip' length 1231795 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[1] 2
* installing *source* package ‘rhdf5’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5.c -o H5.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5A.c -o H5A.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5D.c -o H5D.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5E.c -o H5E.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5F.c -o H5F.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5G.c -o H5G.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5I.c -o H5I.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5L.c -o H5L.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5O.c -o H5O.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5P.c -o H5P.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5S.c -o H5S.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5S_extras.c -o H5S_extras.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5T.c -o H5T.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5Z.c -o H5Z.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c H5constants.c -o H5constants.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c HandleList.cpp -o HandleList.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c HandleListWrap.c -o HandleListWrap.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bit64conversion.c -o bit64conversion.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c external_filters.c -o external_filters.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c h5dump.c -o h5dump.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c h5ls.c -o h5ls.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c h5testLock.c -o h5testLock.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c printdatatype.c -o printdatatype.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wrap.c -o wrap.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o [1] 2 /home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/lib/libhdf5.a /home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/usr/lib/R/lib -lR
g++: error: [1]: No such file or directory
g++: error: 2: No such file or directory
make: *** [/usr/share/R/share/make/shlib.mk:10: rhdf5.so] Error 1
ERROR: compilation failed for package ‘rhdf5’
* removing ‘/home/shared/R/x86_64-pc-linux-gnu-library/4.0/rhdf5’
* restoring previous ‘/home/shared/R/x86_64-pc-linux-gnu-library/4.0/rhdf5’

The downloaded source packages are in
    ‘/tmp/RtmppHSE6d/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    Matrix
  path: /usr/lib/R/site-library
  packages:
    RNetCDF
Old packages: 'bamsignals', 'Cairo', 'ggiraph', 'HDF5Array', 'maftools', 'magick', 'N2R', 'pagoda2', 'proxyC', 'rhdf5', 'Rhtslib', 'rJava', 'RMySQL', 'Rsamtools', 'sccore', 'systemfonts',
  'VariantAnnotation'
Update all/some/none? [a/s/n]: 
n
Warning message:
In .inet_warning(msg) :
  installation of package ‘rhdf5’ had non-zero exit statu

Session info:

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Devuan GNU/Linux 4 (chimaera)

Matrix products: default
BLAS/LAPACK: /usr/local/lib/libflexiblas.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  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] rhdf5_2.36.0        data.table_1.14.2   BiocManager_1.30.16 flexiblas_3.0.0    

loaded via a namespace (and not attached):
[1] compiler_4.1.2     tools_4.1.2        rhdf5filters_1.6.0 Rhdf5lib_1.16.0
rhdf5 • 145 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 7 minutes ago
United States

Looks like you are missing g++. If you have sudo privileges it is easy enough. If not, you will have to ask your sysadmin.

2
Entering edit mode

I think the error is coming from the linking command:

g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o [1] 2 /home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/lib/libhdf5.a /home/shared/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/usr/lib/R/lib -lR

For some reason the command contains [1] and 2 which is why g++ is complaining.

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0
Entering edit mode
sudo apt-get install g++
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
g++ is already the newest version (4:10.2.1-1).

g++ is installed.

I think I found the problem! In my .Rprofile, I have a commad that outputs '[1] 2' (changing the BLAS using flexiblas), and so it seems that was being included in the library path above.

Thanks for your insight!

ADD REPLY
0
Entering edit mode

Glad you found it. It's easy to break R by putting stuff in a startup file like .Rprofile. An easy way to recognize a self-induced issue like this one is to run R with --vanilla. If the issue goes away then you know the culprit is one of your personal startup files.

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