Trouble installing package GO.db
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@c-a-22688
Last seen 17 months ago
University of Louisville

I am writing because I have not been able to install GO.db. I have tried several times with and without updating old packages, and installing updates "from the source the packages need compilation" and not installing updates from source. I keep getting similar errors. Below is the code:

BiocManager::install("GO.db")

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.0 (2019-04-26)
Installing package(s) 'GO.db'
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/GO.db_3.10.0.tar.gz'
Content type 'application/x-gzip' length 31820873 bytes (30.3 MB)
downloaded 30.3 MB

* installing *source* package 'GO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'RSQLite'
Error: package 'AnnotationDbi' could not be loaded
In addition: Warning messages:
1: package 'AnnotationDbi' was built under R version 3.6.1 
2: package 'BiocGenerics' was built under R version 3.6.1 
3: package 'Biobase' was built under R version 3.6.1 
4: package 'IRanges' was built under R version 3.6.1 
5: package 'S4Vectors' was built under R version 3.6.1 
Execution halted
ERROR: lazy loading failed for package 'GO.db'
* removing 'C:/CA Programs/R-3.6.0/library/GO.db'

The downloaded source packages are in
    ‘C:\Users\Carlos\AppData\Local\Temp\RtmpsFjqdI\downloaded_packages’
Old packages: 'fansi', 'mvtnorm', 'stringi'
Update all/some/none? [a/s/n]: 
y
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
        binary source needs_compilation
fansi    0.4.0  0.4.1              TRUE
mvtnorm 1.0-11 1.0-12              TRUE
stringi  1.4.3  1.4.4              TRUE

installing the source packages ‘fansi’, ‘mvtnorm’, ‘stringi’

trying URL 'https://cran.rstudio.com/src/contrib/fansi_0.4.1.tar.gz'
Content type 'application/x-gzip' length 270906 bytes (264 KB)
downloaded 264 KB

trying URL 'https://cran.rstudio.com/src/contrib/mvtnorm_1.0-12.tar.gz'
Content type 'application/x-gzip' length 165938 bytes (162 KB)
downloaded 162 KB

trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.4.4.tar.gz'
Content type 'application/x-gzip' length 7284184 bytes (6.9 MB)
downloaded 6.9 MB

* installing *source* package 'fansi' ...
** package 'fansi' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/CAPROG~1/R-36~1.0/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=generic -c assumptions.c -o assumptions.o
/bin/sh: c:/Rtools/mingw_32/bin/gcc: No such file or directory
make: *** [C:/CAPROG~1/R-36~1.0/etc/i386/Makeconf:208: assumptions.o] Error 127
ERROR: compilation failed for package 'fansi'
* removing 'C:/CA Programs/R-3.6.0/library/fansi'
* restoring previous 'C:/CA Programs/R-3.6.0/library/fansi'
* installing *source* package 'mvtnorm' ...
** package 'mvtnorm' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/CAPROG~1/R-36~1.0/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=generic -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
/bin/sh: c:/Rtools/mingw_32/bin/gcc: No such file or directory
make: *** [C:/CAPROG~1/R-36~1.0/etc/i386/Makeconf:208: C_FORTRAN_interface.o] Error 127
ERROR: compilation failed for package 'mvtnorm'
* removing 'C:/CA Programs/R-3.6.0/library/mvtnorm'
* restoring previous 'C:/CA Programs/R-3.6.0/library/mvtnorm'
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
** using staged installation
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/CAPROG~1/R-36~1.0/include" -DNDEBUG -I. -Iicu61/ -Iicu61/unicode -Iicu61/common -Iicu61/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -DUCONFIG_USE_LOCAL -DU_TOOLUTIL_IMPLEMENTATION -DNDEBUG -DWINVER=0x0600 -D_WIN32_WINNT=0x0600 -DU_USE_STRTOD_L=0         -O2 -Wall  -mtune=generic -c stri_pad.cpp -o stri_pad.o
/bin/sh: c:/Rtools/mingw_32/bin/g++: No such file or directory
make: *** [C:/CAPROG~1/R-36~1.0/etc/i386/Makeconf:215: stri_pad.o] Error 127
ERROR: compilation failed for package 'stringi'
* removing 'C:/CA Programs/R-3.6.0/library/stringi'
* restoring previous 'C:/CA Programs/R-3.6.0/library/stringi'

The downloaded source packages are in
    ‘C:\Users\Carlos\AppData\Local\Temp\RtmpsFjqdI\downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘GO.db’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘fansi’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘mvtnorm’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘stringi’ had non-zero exit status

It looks like fansi, mvtnorm, and stringi were installed, but that may have been from previous attempts where I opted not to update them.

GO.db • 365 views
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You have some packages installed with R version 3.6.1 and you are trying to install in a R version 3.6.0. This might cause your compilation problems. In addition you need to manually install the RSQLite package: (install.packages("RSQLite")). But check if your installation is a good one with BiocManager::valid()

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@james-w-macdonald-5106
Last seen 6 hours ago
United States

The errors that you could use to diagnose are all in the code you present. For example:

Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'RSQLite'
Error: package 'AnnotationDbi' could not be loaded

c:/Rtools/mingw_32/bin/gcc  -I"C:/CAPROG~1/R-36~1.0/include" -DNDEBUG          -O3 -Wall  -std=gnu99 -mtune=generic -c assumptions.c -o assumptions.o
/bin/sh: c:/Rtools/mingw_32/bin/gcc: No such file or directory

c:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/CAPROG~1/R-36~1.0/include" -DNDEBUG -I. -Iicu61/ -Iicu61/unicode -Iicu61/common -Iicu61/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -DUCONFIG_USE_LOCAL -DU_TOOLUTIL_IMPLEMENTATION -DNDEBUG -DWINVER=0x0600 -D_WIN32_WINNT=0x0600 -DU_USE_STRTOD_L=0         -O2 -Wall  -mtune=generic -c stri_pad.cpp -o stri_pad.o
/bin/sh: c:/Rtools/mingw_32/bin/g++: No such file or directory

The first of which indicates you need RSQlite to be installed, which Lluís Revilla Sancho already pointed out. The second and third errors are a little trickier, although a quick google search (of 'c:/Rtools/mingw_32/bin/g++: No such file or directory') should indicate to you that you don't have the Rtools installed, which you will need if you are intending to build source packages with compiled code.

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0
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Another alternative for the Rtools error is that you might have an older version installed, and have neglected to update to the version appropriate for your version of R.

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0
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And another likely problem is spaces in file paths, e.g., CA Programs in

ERROR: lazy loading failed for package 'GO.db'
* removing 'C:/CA Programs/R-3.6.0/library/GO.db'
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