mtmorgan
commented
1 year ago I think your installation is finding the header files for the 'zlib' compression library from the Bioconductor zlibbioc package, but your operating system should be providing zlib. Can you (a) remove.packages("zlibbioc") (b) ensure that libz-dev is available in your operating system, e.g., on Ubuntu sudo apt-get install libz-dev (c) re-install BiocManager::install("zlibbioc") and then BiocManager::install("ShortRead")?
When install ShortRead by BiocManager::install(), and R version is 4.2.1, this package is not successful installed, and detail is as follow:\ `installing to /home/xinzhepang/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ShortRead/00new/ShortRead/libs R inst byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘ShortRead’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/xxx/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ShortRead/00new/ShortRead/libs/ShortRead.so': /home/xxx/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ShortRead/00new/ShortRead/libs/ShortRead.so: undefined symbol: bioc_gzread Error: loading failed Execution halted ERROR: loading failed
The downloaded source packages are in ‘/tmp/RtmpteFAiR/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: foreign, MASS, mgcv, rpart, spatial Warning message: In install.packages(...) : installation of package ‘ShortRead’ had non-zero exit status`