Common problems and their solutions (hopefully 🤞🏼)

[jhrcook]

Problem: Unable to install Bioconductor packages because some library can't be found.

Specifically, I had this problem with installing 'XVector' and receiving the following error:

...
gcc -I"/n/app/R/4.1.1/lib64/R/include" -DNDEBUG  -I'/n/data1/hms/dbmi/park/Cook/speclet/renv/library/R-4.1/x86_64-pc-linux-gnu/S4Vectors/include' -I'/n/data1/hms/dbmi/park/Cook/speclet/renv/library/R-4.1/x86_64-pc-linux-gnu/IRanges/include' -I/n/app/pcre2/10.34/include -I/n/app/cairo/1.14.6/include/cairo -I/n/app/tiff/4.0.7/include -I/n/app/jpeg/9b/include -I/n/app/openblas/0.2.19/include -I/n/app/libpng/1.6.26/include -I/n/app/xz/5.2.3/include -I/n/app/gsl/2.3/include -I/n/app/hdf5/1.10.1/include -I/n/app/boost/1.62.0/include -I /n/app/pango/1.40.3/include   -fpic  -g -O2  -c XVector_class.c -o XVector_class.o
gcc -I"/n/app/R/4.1.1/lib64/R/include" -DNDEBUG  -I'/n/data1/hms/dbmi/park/Cook/speclet/renv/library/R-4.1/x86_64-pc-linux-gnu/S4Vectors/include' -I'/n/data1/hms/dbmi/park/Cook/speclet/renv/library/R-4.1/x86_64-pc-linux-gnu/IRanges/include' -I/n/app/pcre2/10.34/include -I/n/app/cairo/1.14.6/include/cairo -I/n/app/tiff/4.0.7/include -I/n/app/jpeg/9b/include -I/n/app/openblas/0.2.19/include -I/n/app/libpng/1.6.26/include -I/n/app/xz/5.2.3/include -I/n/app/gsl/2.3/include -I/n/app/hdf5/1.10.1/include -I/n/app/boost/1.62.0/include -I /n/app/pango/1.40.3/include   -fpic  -g -O2  -c io_utils.c -o io_utils.o
io_utils.c:16:10: fatal error: zlib.h: No such file or directory
   16 | #include <zlib.h>
      |          ^~~~~~~~
compilation terminated.
make: *** [io_utils.o] Error 1
ERROR: compilation failed for package ‘XVector’
* removing ‘/n/data1/hms/dbmi/park/Cook/speclet/renv/library/R-4.1/x86_64-pc-linux-gnu/XVector’

Solution

1. deactivate the conda environment
2. exit the current directory to one without an 'renv' controlled environment
3. install 'BiocManager': install.packages("BiocManager")
4. install 'XVector': BiocManager::install("biomaRt")

If that doesn't work, try uninstalling 'XVector' and then installing it. When I figured out the solution, I had just started a new default library for R (~/R-4.1/library), so the fresh library may have also played a role.