| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:53 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
|
To the developers/maintainers of the VariantAnnotation package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2122/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantAnnotation 1.45.1 (landing page) Bioconductor Package Maintainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: VariantAnnotation |
| Version: 1.45.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings VariantAnnotation_1.45.1.tar.gz |
| StartedAt: 2023-02-28 18:24:26 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 18:38:38 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 852.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: VariantAnnotation.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings VariantAnnotation_1.45.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/VariantAnnotation.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantAnnotation’ version ‘1.45.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'MatrixGenerics', 'GenomeInfoDb', 'GenomicRanges',
'SummarizedExperiment', 'Rsamtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VariantAnnotation’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
R 2.2Mb
extdata 1.2Mb
libs 3.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’
‘Rsamtools:::.RsamtoolsFile’ ‘Rsamtools:::.RsamtoolsFileList’
‘Rsamtools:::.io_check_exists’ ‘S4Vectors:::expandByColumnSet’
‘S4Vectors:::labeledLine’ ‘S4Vectors:::recycleVector’
‘S4Vectors:::selectSome’
‘SummarizedExperiment:::.SummarizedExperiment.charbound’
‘SummarizedExperiment:::.cbind.DataFrame’
‘rtracklayer:::checkArgFormat’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
VRangesForMatching: no visible binding for global variable ‘REF’
VRangesForMatching: no visible binding for global variable ‘ALT’
Undefined global functions or variables:
ALT REF
* checking Rd files ... WARNING
checkRd: (5) PROVEANDb-class.Rd:24-27: \item in \describe must have non-empty label
checkRd: (5) PROVEANDb-class.Rd:28-32: \item in \describe must have non-empty label
checkRd: (5) PROVEANDb-class.Rd:33-37: \item in \describe must have non-empty label
checkRd: (5) PROVEANDb-class.Rd:38-42: \item in \describe must have non-empty label
checkRd: (5) PROVEANDb-class.Rd:43-49: \item in \describe must have non-empty label
checkRd: (5) PolyPhenDb-class.Rd:25-28: \item in \describe must have non-empty label
checkRd: (5) PolyPhenDb-class.Rd:29-33: \item in \describe must have non-empty label
checkRd: (5) PolyPhenDb-class.Rd:34-38: \item in \describe must have non-empty label
checkRd: (5) PolyPhenDb-class.Rd:39-45: \item in \describe must have non-empty label
checkRd: (5) PolyPhenDb-class.Rd:46-52: \item in \describe must have non-empty label
checkRd: (5) SIFTDb-class.Rd:24-27: \item in \describe must have non-empty label
checkRd: (5) SIFTDb-class.Rd:28-32: \item in \describe must have non-empty label
checkRd: (5) SIFTDb-class.Rd:33-37: \item in \describe must have non-empty label
checkRd: (5) SIFTDb-class.Rd:38-44: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:107-109: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:110-121: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:129-170: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:171-177: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:178-183: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:184-188: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:189-197: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:198-204: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:205-211: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:212-216: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:217-221: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:222-226: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:227-240: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:241-246: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:254-258: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:259-266: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:267-284: \item in \describe must have non-empty label
checkRd: (5) VCF-class.Rd:291-304: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:47-51: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:58-61: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:62-66: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:67-86: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:87-94: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:95-100: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:101-106: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:107-111: \item in \describe must have non-empty label
checkRd: (5) VCFHeader-class.Rd:112-118: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:146-178: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:179-224: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:232-265: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:266-268: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:269-281: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:290-292: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:293-295: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:296-299: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:300-303: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:304-307: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:308-310: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:311-314: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:315-319: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:320-322: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:323-326: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:327-330: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:336-339: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:340-344: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:345-349: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:355-358: \item in \describe must have non-empty label
checkRd: (5) VRanges-class.Rd:359-372: \item in \describe must have non-empty label
checkRd: (5) VRangesList-class.Rd:35-38: \item in \describe must have non-empty label
checkRd: (5) VRangesList-class.Rd:44-47: \item in \describe must have non-empty label
checkRd: (5) VRangesList-class.Rd:48-52: \item in \describe must have non-empty label
checkRd: (5) VRangesList-class.Rd:58-62: \item in \describe must have non-empty label
checkRd: (5) VariantType-class.Rd:134-138: \item in \describe must have non-empty label
checkRd: (5) VariantType-class.Rd:139-143: \item in \describe must have non-empty label
checkRd: (5) VariantType-class.Rd:144-149: \item in \describe must have non-empty label
checkRd: (5) VariantType-class.Rd:150-154: \item in \describe must have non-empty label
checkRd: (5) VariantType-class.Rd:155-159: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:31-34: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:35-37: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:42-43: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:44-45: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:46-47: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:48-49: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:50-51: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:52-54: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:59-60: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:61-62: \item in \describe must have non-empty label
checkRd: (5) VcfFile-class.Rd:67-69: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/VariantAnnotation/libs/VariantAnnotation.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘VariantAnnotation/libs/VariantAnnotation.so’:
Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
locateVariants-methods 26.986 1.120 28.110
predictCoding-methods 23.346 0.496 23.846
summarizeVariants-methods 7.839 0.136 7.977
PROVEANDb-class 4.822 0.651 8.333
filterVcf-methods 3.367 0.288 10.730
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘VariantAnnotation_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘VariantAnnotation.Rnw’... OK
‘filterVcf.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.
VariantAnnotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘VariantAnnotation’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c dna_hash.c -o dna_hash.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c strhash.c -o strhash.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utilities.c -o utilities.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vcffile.c -o vcffile.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vcftype.c -o vcftype.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c writevcf.c -o writevcf.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/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/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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)
VariantAnnotation.Rcheck/tests/VariantAnnotation_unit_tests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("VariantAnnotation") || stop("unable to load VariantAnnotation package")
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
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colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
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Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
[1] TRUE
> VariantAnnotation:::.test()
Loading required package: RSQLite
[W::tbx_parse1] VCF INFO/END=2827680 is smaller than POS at 1:2827692
This tag will be ignored. Note: only one invalid END tag will be reported.
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/TS" is invalid, forcing Number=0
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/TS" is invalid, forcing Number=0
starting prefilter
prefiltering 10376 records
prefiltered to /tmp/RtmpUzTwAQ/file2ac2eb769c3823
compressing and indexing '/tmp/RtmpUzTwAQ/file2ac2eb769c3823'
starting filter
filtering 10376 records
completed filtering
compressing and indexing '/tmp/RtmpUzTwAQ/file2ac2eb34b273bd'
Loading required package: survival
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:VariantAnnotation':
expand
The following object is masked from 'package:S4Vectors':
expand
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
'select()' returned 1:1 mapping between keys and columns
Loading required package: BSgenome
Loading required package: rtracklayer
'select()' returned many:1 mapping between keys and columns
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
RUNIT TEST PROTOCOL -- Tue Feb 28 18:33:49 2023
***********************************************
Number of test functions: 100
Number of errors: 0
Number of failures: 0
1 Test Suite :
VariantAnnotation RUnit Tests - 100 test functions, 0 errors, 0 failures
Number of test functions: 100
Number of errors: 0
Number of failures: 0
Warning messages:
1: info fields with no header: noMatch
2: In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
3: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 7 out-of-bound ranges located on sequence
70477. Note that ranges located on a sequence whose length is unknown
(NA) or on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 6 out-of-bound ranges located on sequence
70477. Note that ranges located on a sequence whose length is unknown
(NA) or on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
>
> proc.time()
user system elapsed
148.828 2.901 153.788
VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings
| name | user | system | elapsed | |
| GLtoGP | 1.605 | 0.196 | 1.803 | |
| PROVEANDb-class | 4.822 | 0.651 | 8.333 | |
| PolyPhenDb-class | 2.253 | 0.195 | 3.999 | |
| SIFTDb-class | 0.001 | 0.000 | 0.001 | |
| ScanVcfParam-class | 1.249 | 0.012 | 1.262 | |
| VCF-class | 2.146 | 0.092 | 2.240 | |
| VCFHeader-class | 0.11 | 0.00 | 0.11 | |
| VRanges-class | 0.611 | 0.032 | 0.642 | |
| VRangesList-class | 0.587 | 0.020 | 0.610 | |
| VariantType-class | 0.01 | 0.00 | 0.01 | |
| VcfFile-class | 0.742 | 0.028 | 0.771 | |
| filterVcf-methods | 3.367 | 0.288 | 10.730 | |
| genotypeToSnpMatrix-methods | 1.761 | 0.156 | 1.918 | |
| getTranscriptSeqs-methods | 0 | 0 | 0 | |
| indexVcf-method | 0.005 | 0.005 | 0.010 | |
| isSNV-methods | 1.20 | 0.06 | 1.26 | |
| locateVariants-methods | 26.986 | 1.120 | 28.110 | |
| predictCoding-methods | 23.346 | 0.496 | 23.846 | |
| probabilityToSnpMatrix | 0.001 | 0.000 | 0.001 | |
| readVcf-methods | 4.862 | 0.088 | 4.951 | |
| scanVcf-methods | 0.307 | 0.012 | 0.319 | |
| seqinfo-method | 0.085 | 0.004 | 0.088 | |
| snpSummary | 0.404 | 0.004 | 0.409 | |
| summarizeVariants-methods | 7.839 | 0.136 | 7.977 | |
| writeVcf-methods | 2.317 | 0.012 | 2.329 | |