GenomicFeatures 1.22.0
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 109600 / Revision: 109947 | | Last Changed Date: 2015-10-13 17:17:51 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 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 && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.22.0.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out && C:\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_1.22.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.22.0'
* 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' ... [465s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
coverageByTranscript 48.74 5.78 54.55
coordinate-mapping-methods 42.56 1.45 67.25
makeTxDbFromBiomart 25.78 1.14 121.23
makeFeatureDbFromUCSC 14.78 0.84 120.62
extractTranscriptSeqs 8.58 0.08 8.84
makeTxDbFromUCSC 7.84 0.14 55.38
transcriptLocs2refLocs 7.08 0.14 7.25
extractUpstreamSeqs 1.92 0.24 6.46
** running examples for arch 'x64' ... [453s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
coverageByTranscript 43.05 5.06 48.17
coordinate-mapping-methods 35.64 0.92 36.56
makeTxDbFromBiomart 26.25 1.22 113.28
makeFeatureDbFromUCSC 15.41 1.49 153.44
extractTranscriptSeqs 9.79 0.03 9.83
transcriptLocs2refLocs 7.14 0.08 7.21
makeTxDbFromUCSC 6.90 0.14 57.96
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'GenomicFeatures_unit_tests.R' [119s]
[119s] OK
** running tests for arch 'x64' ...
Running 'GenomicFeatures_unit_tests.R' [131s]
[131s] 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
'C:/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_1.22.0.zip
* DONE (GenomicFeatures)