Entering edit mode
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.
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 withBiocManager::valid()