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This page was generated on 2023-06-01 18:17:20 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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 | ||||
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To the developers/maintainers of the VariantAnnotation package: Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 87/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| VariantAnnotation 1.47.0 (landing page) Bioconductor Package Maintainer
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | WARNINGS | ||||||||
| Package: VariantAnnotation |
| Version: 1.47.0 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL VariantAnnotation |
| StartedAt: 2023-06-01 12:27:29 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 12:28:46 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 77.0 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’ * installing *source* package ‘VariantAnnotation’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’ gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/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/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/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/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/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/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/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/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/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/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c strhash.c -o strhash.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utilities.c -o utilities.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c vcffile.c -o vcffile.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c vcftype.c -o vcftype.o gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/XVector/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Biostrings/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c writevcf.c -o writevcf.o gcc -shared -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-testing/Rlibs/Rhtslib/usrlib/libhts.a -lcurl installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/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)