Michael Lawrence
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/VariantTools |
| Branch: RELEASE_3_12 |
| Last Commit: ed6c8be |
| Last Changed Date: 2020-10-27 10:47:52 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:09 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the VariantTools package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1933/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantTools 1.32.0 (landing page) Michael Lawrence
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: VariantTools |
| Version: 1.32.0 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings VariantTools_1.32.0.tar.gz |
| StartedAt: 2021-05-06 07:51:16 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 08:01:16 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 600.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: VariantTools.Rcheck |
| Warnings: 2 |
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### Running command:
###
### set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings VariantTools_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantTools.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VariantTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantTools' version '1.32.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'gmapR'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'VariantTools' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/callVariants.Rd:84: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/extractCoverageForPositions.Rd:16: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/pileupVariants.Rd:21: file link 'PileupFiles' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/pileupVariants.Rd:28: file link 'ApplyPileupsParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/postFilterVariants.Rd:50: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/qaVariants.Rd:51: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/tallyVariants.Rd:60: file link 'stackSamples' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:8: file link 'VCF' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:10: file link 'writeVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:19: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantTools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
doc 5.4Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:::testPackage' 'IRanges:::unlist_as_integer'
See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: 'gmapR'
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
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable 'control.alt.depth'
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
global variable 'control.total.depth'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable 'read.pos.mean'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable 'read.pos.mean.ref'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable 'read.pos.var'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
variable 'read.pos.var.ref'
ReadPositionTTestFilter : <anonymous>: no visible global function
definition for 'rawDepth'
StrandFETFilter : <anonymous>: no visible binding for global variable
'count.plus.ref'
StrandFETFilter : <anonymous>: no visible binding for global variable
'count.minus.ref'
StrandFETFilter : <anonymous>: no visible binding for global variable
'count.plus'
StrandFETFilter : <anonymous>: no visible binding for global variable
'count.minus'
calculateConcordanceMatrix: no visible binding for global variable 'x'
caseControlFET: no visible binding for global variable
'control.alt.depth'
caseControlFET: no visible binding for global variable
'control.total.depth'
variantGR2Vcf: no visible global function definition for
'variantGRangesIsDeprecated'
variantGR2Vcf: no visible global function definition for
'makeVRangesFromVariantGRanges'
callVariants,GenomicRanges: no visible global function definition for
'variantGRangesIsDeprecated'
callVariants,GenomicRanges: no visible global function definition for
'variantGRangesToVRanges'
Undefined global functions or variables:
control.alt.depth control.total.depth count.minus count.minus.ref
count.plus count.plus.ref makeVRangesFromVariantGRanges rawDepth
read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
variantGRangesIsDeprecated variantGRangesToVRanges x
* checking Rd files ... WARNING
man/tallyVariants.Rd: non-ASCII input and no declared encoding
problem found in 'tallyVariants.Rd'
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'gmapR'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
'fig'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callGenotypes 5.02 0.36 76.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callGenotypes 4.7 0.19 85.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'VariantTools_unit_tests.R'
OK
** running tests for arch 'x64' ...
Running 'VariantTools_unit_tests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 7 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantTools.Rcheck/00check.log'
for details.
VariantTools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/VariantTools_1.32.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.32.0.zip && rm VariantTools_1.32.0.tar.gz VariantTools_1.32.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 5966k 100 5966k 0 0 72.9M 0 --:--:-- --:--:-- --:--:-- 73.7M
install for i386
* installing *source* package 'VariantTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'VariantTools'
finding HTML links ... done
FilterConstructors html
annnotateWithControlDepth html
callGenotypes html
callSampleSpecificVariants html
callVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/callVariants.Rd:84: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
callWildtype html
concordance html
extractCoverageForPositions html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/extractCoverageForPositions.Rd:16: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
matchVariants html
pileupVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/pileupVariants.Rd:21: file link 'PileupFiles' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/pileupVariants.Rd:28: file link 'ApplyPileupsParam' in package 'Rsamtools' does not exist and so has been treated as a topic
postFilterVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/postFilterVariants.Rd:50: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
qaVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/qaVariants.Rd:51: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
tallyVariants html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/tallyVariants.Rd:60: file link 'stackSamples' in package 'VariantAnnotation' does not exist and so has been treated as a topic
variantGR2Vcf html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:8: file link 'VCF' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:10: file link 'writeVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:19: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
vignette html
** building package indices
** installing vignettes
'VariantTools.Rnw'
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'VariantTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantTools' as VariantTools_1.32.0.zip
* DONE (VariantTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'VariantTools' successfully unpacked and MD5 sums checked
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VariantTools.Rcheck/tests_i386/VariantTools_unit_tests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("VariantTools") || stop("unable to load VariantTools package")
> ##VariantTools:::.test()
>
> proc.time()
user system elapsed
0.23 0.01 0.23
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VariantTools.Rcheck/tests_x64/VariantTools_unit_tests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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("VariantTools") || stop("unable to load VariantTools package")
> ##VariantTools:::.test()
>
> proc.time()
user system elapsed
0.21 0.04 0.25
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VariantTools.Rcheck/examples_i386/VariantTools-Ex.timings
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VariantTools.Rcheck/examples_x64/VariantTools-Ex.timings
|