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BioC 3.0: CHECK report for GenomicFeatures on moscato1

This page was generated on 2015-04-10 09:45:58 -0700 (Fri, 10 Apr 2015).

Package 367/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.18.7
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomicFeatures
Last Changed Rev: 102060 / Revision: 102249
Last Changed Date: 2015-04-07 14:45:31 -0700 (Tue, 07 Apr 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: GenomicFeatures
Version: 1.18.7
Command: rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.18.7.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.18.7.tar.gz
StartedAt: 2015-04-10 01:31:47 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:47:16 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 929.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicFeatures.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.18.7.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.18.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.18.7'
* 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:
  'BiocGenerics:::testPackage'
  'GenomicRanges:::unsafe.transcriptLocs2refLocs'
  'GenomicRanges:::unsafe.transcriptWidths' 'S4Vectors:::V_recycle'
  'S4Vectors:::duplicatedIntegerQuads' 'S4Vectors:::fancy_mseq'
  'S4Vectors:::matchIntegerQuads' 'S4Vectors:::orderIntegerQuads'
  'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
  '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
.extractTranscriptSeqsFromOneSeq: no visible global function definition
  for 'getSeq'
.extract_and_combine: no visible global function definition for
  'getSeq'
.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'
getPromoterSeq,GRanges: no visible global function definition for
  'getSeq'
getPromoterSeq,GRangesList: no visible global function definition for
  'getSeq'
* checking Rd files ... OK
* 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' ... [206s] WARNING
Found the following significant warnings:

  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                             user system elapsed
extractTranscriptSeqs       15.56   0.06   15.63
transcriptLocs2refLocs       9.08   0.16    9.25
makeFeatureDbFromUCSC        6.68   0.26   76.58
extractUpstreamSeqs          5.98   0.18   19.13
makeTranscriptDbFromBiomart  4.28   0.05   23.62
makeTranscriptDbFromUCSC     2.95   0.05   35.99
** running examples for arch 'x64' ... [194s] WARNING
Found the following significant warnings:

  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                             user system elapsed
extractTranscriptSeqs       13.23   0.11   13.34
transcriptLocs2refLocs       9.24   0.07    9.31
makeFeatureDbFromUCSC        7.38   0.45   78.06
extractUpstreamSeqs          5.16   0.14    5.31
makeTranscriptDbFromBiomart  5.07   0.08   22.59
makeTranscriptDbFromUCSC     2.26   0.03   38.51
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'GenomicFeatures_unit_tests.R' [107s]
 [108s] OK
** running tests for arch 'x64' ...
  Running 'GenomicFeatures_unit_tests.R' [123s]
 [124s] 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

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.

GenomicFeatures.Rcheck/00install.out:


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_1.18.7.zip
* DONE (GenomicFeatures)

GenomicFeatures.Rcheck/examples_i386/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.050.000.05
TxDb-class1.250.312.23
as-format-methods1.520.091.61
extractTranscriptSeqs15.56 0.0615.63
extractUpstreamSeqs 5.98 0.1819.13
features0.090.000.09
getPromoterSeq-methods1.820.091.91
id2name0.080.020.10
makeFeatureDbFromUCSC 6.68 0.2676.58
makeTranscriptDb0.090.000.09
makeTranscriptDbFromBiomart 4.28 0.0523.62
makeTranscriptDbFromGFF2.040.012.06
makeTranscriptDbFromUCSC 2.95 0.0535.99
makeTxDbPackage0.480.050.97
nearest-methods0.810.010.82
select-methods0.250.000.25
transcriptLocs2refLocs9.080.169.25
transcripts1.960.052.01
transcriptsBy0.630.000.63
transcriptsByOverlaps0.510.000.51

GenomicFeatures.Rcheck/examples_x64/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.030.000.03
TxDb-class1.150.174.69
as-format-methods1.230.031.27
extractTranscriptSeqs13.23 0.1113.34
extractUpstreamSeqs5.160.145.31
features0.060.020.07
getPromoterSeq-methods1.210.121.33
id2name0.050.020.06
makeFeatureDbFromUCSC 7.38 0.4578.06
makeTranscriptDb0.090.000.09
makeTranscriptDbFromBiomart 5.07 0.0822.59
makeTranscriptDbFromGFF1.470.031.50
makeTranscriptDbFromUCSC 2.26 0.0338.51
makeTxDbPackage0.380.020.39
nearest-methods0.500.050.54
select-methods0.160.000.16
transcriptLocs2refLocs9.240.079.31
transcripts1.820.052.86
transcriptsBy0.670.000.67
transcriptsByOverlaps0.240.000.23