| Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 113/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| VariantAnnotation 1.48.1 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
To the developers/maintainers of the VariantAnnotation package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: VariantAnnotation |
| Version: 1.48.1 |
| Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL VariantAnnotation |
| StartedAt: 2024-03-08 15:34:00 -0500 (Fri, 08 Mar 2024) |
| EndedAt: 2024-03-08 15:35:13 -0500 (Fri, 08 Mar 2024) |
| EllapsedTime: 73.7 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’ * installing *source* package ‘VariantAnnotation’ ... ** using staged installation ** libs gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c dna_hash.c -o dna_hash.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c strhash.c -o strhash.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utilities.c -o utilities.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c vcffile.c -o vcffile.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c vcftype.c -o vcftype.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/XVector/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c writevcf.c -o writevcf.o gcc -shared -L/home/hpages/bbs-3.18-bioc-R41/R/lib -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR installing to /home/hpages/bbs-3.18-bioc-R41/R/site-library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (VariantAnnotation)