VariantTools 1.18.1
Michael Lawrence
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/VariantTools | | Last Changed Rev: 129867 / Revision: 131943 | | Last Changed Date: 2017-05-25 13:47:56 -0400 (Thu, 25 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf VariantTools.buildbin-libdir VariantTools.Rcheck && mkdir VariantTools.buildbin-libdir VariantTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VariantTools.buildbin-libdir VariantTools_1.18.1.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-3.5-bioc\R\bin\R.exe CMD check --library=VariantTools.buildbin-libdir --install="check:VariantTools-install.out" --force-multiarch --no-vignettes --timings VariantTools_1.18.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/VariantTools.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.18.1'
* 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 6.4Mb
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
callGenotypes 2.66 0.24 25.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
callGenotypes 3.69 0.11 34.73
* 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: 7 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/VariantTools.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'VariantTools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'VariantTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantTools' as VariantTools_1.18.1.zip
* DONE (VariantTools)