| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:27 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the VariantTools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantTools.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1998/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantTools 1.34.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: VariantTools |
| Version: 1.34.0 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VariantTools_1.34.0.tar.gz |
| StartedAt: 2021-10-15 07:07:39 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 07:15:51 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 491.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: VariantTools.Rcheck |
| Warnings: 1 |
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### Running command:
###
### set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VariantTools_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/VariantTools.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.34.0'
* 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 ... OK
* checking installed package size ... NOTE
installed size is 6.6Mb
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 3.32 0.08 64.27
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callGenotypes 3.49 0.11 65.69
* 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: 1 WARNING, 7 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-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://155.52.207.165/BBS/3.13/bioc/src/contrib/VariantTools_1.34.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.34.0.zip && rm VariantTools_1.34.0.tar.gz VariantTools_1.34.0.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
51 5977k 51 3055k 0 0 3310k 0 0:00:01 --:--:-- 0:00:01 3310k
100 5977k 100 5977k 0 0 3937k 0 0:00:01 0:00:01 --:--:-- 3940k
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
callWildtype html
concordance html
extractCoverageForPositions html
matchVariants html
pileupVariants html
postFilterVariants html
qaVariants html
tallyVariants html
finding level-2 HTML links ... done
variantGR2Vcf html
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_1.34.0.zip
* DONE (VariantTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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
0.25 0.06 0.29
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VariantTools.Rcheck/tests_x64/VariantTools_unit_tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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
0.25 0.04 0.28
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VariantTools.Rcheck/examples_i386/VariantTools-Ex.timings
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VariantTools.Rcheck/examples_x64/VariantTools-Ex.timings
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