GenomicFeatures 1.21.18
Bioconductor Package Maintainer
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 107563 / Revision: 107602 | | Last Changed Date: 2015-08-18 15:57:24 -0700 (Tue, 18 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.21.18.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.21.18.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.21.18'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
'AnnotationDbi'
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 whether package 'GenomicFeatures' can be installed ... OK
* checking installed package size ... OK
* 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
'library' or 'require' calls in package code:
'FDb.UCSC.tRNAs' 'mirbase.db'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
'AnnotationDbi:::.getMetaValue' 'AnnotationDbi:::.resort'
'AnnotationDbi:::.testForValidKeytype'
'AnnotationDbi:::.testSelectArgs' 'AnnotationDbi:::.valid.colnames'
'AnnotationDbi:::.valid.metadata.table'
'AnnotationDbi:::.valid.table.colnames' 'AnnotationDbi:::dbEasyQuery'
'AnnotationDbi:::dbQuery' 'AnnotationDbi:::smartKeys'
'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
'rtracklayer:::resourceDescription' 'rtracklayer:::ucscTableOutputs'
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
.microRNAs: no visible global function definition for 'mirbase_dbconn'
supportedMiRBaseBuildValues: no visible global function definition for
'toTable'
supportedMiRBaseBuildValues: no visible binding for global variable
'mirbaseSPECIES'
* checking Rd files ... NOTE
prepare_Rd: makeTxDbFromGRanges.Rd:43-44: Dropping empty section \details
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [491s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
coordinate-mapping-methods 57.56 1.42 104.49
makeTxDbFromBiomart 36.85 1.16 165.82
makeFeatureDbFromUCSC 16.62 0.62 90.82
makeTxDbFromUCSC 12.50 0.16 51.14
extractTranscriptSeqs 12.40 0.06 13.02
transcriptLocs2refLocs 10.68 0.16 20.69
makeTxDbFromGFF 8.42 0.07 9.05
transcriptLengths 6.16 0.11 6.27
extractUpstreamSeqs 3.31 0.27 5.74
** running examples for arch 'x64' ... [483s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
coordinate-mapping-methods 53.62 1.12 56.03
makeTxDbFromBiomart 40.59 1.51 208.88
makeFeatureDbFromUCSC 17.26 1.00 94.77
extractTranscriptSeqs 15.60 0.10 15.71
makeTxDbFromUCSC 12.01 0.27 47.51
transcriptLocs2refLocs 12.03 0.06 12.07
makeTxDbFromGFF 7.41 0.13 8.15
transcriptLengths 5.26 0.26 5.53
makeTxDbFromGRanges 4.90 0.01 5.43
TxDb-class 1.10 0.17 5.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'GenomicFeatures_unit_tests.R' [194s]
[194s] OK
** running tests for arch 'x64' ...
Running 'GenomicFeatures_unit_tests.R' [201s]
[201s] 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: 4 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GenomicFeatures' ...
** R
** 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 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.21.18.zip
* DONE (GenomicFeatures)