Michael Lawrence
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/VariantTools |
| Branch: RELEASE_3_6 |
| Last Commit: 88453a2 |
| Last Changed Date: 2017-10-30 12:39:54 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:22:13 -0400 (Thu, 12 Apr 2018).
| Package 1445/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| VariantTools 1.20.0 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: VariantTools |
| Version: 1.20.0 |
| Command: rm -rf VariantTools.buildbin-libdir VariantTools.Rcheck && mkdir VariantTools.buildbin-libdir VariantTools.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VariantTools.buildbin-libdir VariantTools_1.20.0.tar.gz >VariantTools.Rcheck\00install.out 2>&1 && cp VariantTools.Rcheck\00install.out VariantTools-install.out && set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=VariantTools.buildbin-libdir --install="check:VariantTools-install.out" --force-multiarch --no-vignettes --timings VariantTools_1.20.0.tar.gz |
| StartedAt: 2018-04-12 03:46:33 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:53:06 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 392.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: VariantTools.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf VariantTools.buildbin-libdir VariantTools.Rcheck && mkdir VariantTools.buildbin-libdir VariantTools.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VariantTools.buildbin-libdir VariantTools_1.20.0.tar.gz >VariantTools.Rcheck\00install.out 2>&1 && cp VariantTools.Rcheck\00install.out VariantTools-install.out && set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=VariantTools.buildbin-libdir --install="check:VariantTools-install.out" --force-multiarch --no-vignettes --timings VariantTools_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/VariantTools.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.20.0'
* 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-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/callVariants.Rd:84: missing file link 'FilterRules'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/extractCoverageForPositions.Rd:16: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/pileupVariants.Rd:21: missing file link 'PileupFiles'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/pileupVariants.Rd:28: missing file link 'ApplyPileupsParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/postFilterVariants.Rd:50: missing file link 'FilterRules'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/qaVariants.Rd:51: missing file link 'FilterRules'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/tallyVariants.Rd:46: missing file link 'stackSamples'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/variantGR2Vcf.Rd:8: missing file link 'VCF'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/variantGR2Vcf.Rd:10: missing file link 'writeVcf'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/variantGR2Vcf.Rd:19: missing file link 'VRanges'
See 'C:/Users/biocbuild/bbs-3.6-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 5.6Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
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'
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
* checking Rd files ... OK
* 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 or elapsed time > 5s
user system elapsed
FilterConstructors 2.51 0.03 6.86
callGenotypes 2.33 0.16 25.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
callGenotypes 2.77 0.14 26.14
* 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-3.6-bioc/meat/VariantTools.Rcheck/00check.log'
for details.
VariantTools.Rcheck/00install.out
install for i386
* installing *source* package 'VariantTools' ...
** R
** data
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/callVariants.Rd:84: missing file link 'FilterRules'
callWildtype html
concordance html
extractCoverageForPositions html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/extractCoverageForPositions.Rd:16: missing file link 'coverage'
matchVariants html
pileupVariants html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/pileupVariants.Rd:21: missing file link 'PileupFiles'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/pileupVariants.Rd:28: missing file link 'ApplyPileupsParam'
postFilterVariants html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/postFilterVariants.Rd:50: missing file link 'FilterRules'
qaVariants html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/qaVariants.Rd:51: missing file link 'FilterRules'
tallyVariants html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/tallyVariants.Rd:46: missing file link 'stackSamples'
variantGR2Vcf html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/variantGR2Vcf.Rd:8: missing file link 'VCF'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/variantGR2Vcf.Rd:10: missing file link 'writeVcf'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpI1gEyh/R.INSTALL3a0070d36552/VariantTools/man/variantGR2Vcf.Rd:19: missing file link 'VRanges'
vignette html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'VariantTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantTools' as VariantTools_1.20.0.zip
* DONE (VariantTools)
In R CMD INSTALL
In R CMD INSTALL
|
VariantTools.Rcheck/tests_i386/VariantTools_unit_tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
0.18 0.04 0.21
|
VariantTools.Rcheck/tests_x64/VariantTools_unit_tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 0.03 0.25
|
|
VariantTools.Rcheck/examples_i386/VariantTools-Ex.timings
|
VariantTools.Rcheck/examples_x64/VariantTools-Ex.timings
|