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BioC 2.13: CHECK report for GenomicFeatures on moscato1

This page was generated on 2014-04-05 09:49:57 -0700 (Sat, 05 Apr 2014).

Package 299/750HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.14.5
Bioconductor Package Maintainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GenomicFeatures
Last Changed Rev: 87404 / Revision: 88450
Last Changed Date: 2014-03-13 10:55:47 -0700 (Thu, 13 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GenomicFeatures
Version: 1.14.5
Command: rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.14.5.tar.gz >GenomicFeatures-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.14.5.tar.gz && mv GenomicFeatures.buildbin-libdir/* GenomicFeatures.Rcheck/ && rmdir GenomicFeatures.buildbin-libdir
StartedAt: 2014-04-05 04:09:09 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:29:54 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 1244.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GenomicFeatures.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.14.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'IRanges' 'GenomicRanges' 'rtracklayer' 'biomaRt' 'Biostrings'
A package should be listed in only one of these fields.
* 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
':::' calls which should be '::':
  'DBI:::dbGetQuery' 'DBI:::dbListFields' 'DBI:::dbListTables'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Biostrings:::getDNAComplementLookup' 'biomaRt:::martBM'
  'biomaRt:::martDataset' 'biomaRt:::martHost'
  'rtracklayer:::ucscTableOutputs'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.keys' '.reverseColAbbreviations'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.setseqnameStyle: no visible binding for global variable 'txdb'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'GenomicFeatures.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [298s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 109.44   6.73  122.91
makeFeatureDbFromUCSC          8.70   0.17   82.73
makeTranscriptDbFromUCSC       5.76   0.03   45.96
makeTranscriptDbFromBiomart    2.15   0.04   19.06
** running examples for arch 'x64' ... [319s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 112.78   9.83  122.62
makeFeatureDbFromUCSC         13.46   0.28   88.22
makeTranscriptDbFromUCSC       7.27   0.02   47.33
makeTranscriptDbFromBiomart    3.31   0.01   25.54
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'GenomicFeatures_unit_tests.R' [169s]
 [170s] OK
** running tests for arch 'x64'
  Running 'GenomicFeatures_unit_tests.R' [161s]
 [161s] 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-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_1.14.5.zip
* DONE (GenomicFeatures)

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

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.060.000.06
TranscriptDb-class1.280.281.63
as-format-methods1.910.001.90
extractTranscriptsFromGenome109.44 6.73122.91
features0.090.000.09
getPromoterSeq-methods3.900.214.53
id2name0.110.000.11
makeFeatureDbFromUCSC 8.70 0.1782.73
makeTranscriptDb0.110.000.11
makeTranscriptDbFromBiomart 2.15 0.0419.06
makeTranscriptDbFromGFF2.000.072.06
makeTranscriptDbFromUCSC 5.76 0.0345.96
makeTxDbPackage0.430.000.79
nearest-methods1.170.001.19
saveFeatures000
select-methods0.210.030.23
transcripts2.780.002.78
transcriptsBy1.980.021.99
transcriptsByOverlaps0.410.010.42

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

nameusersystemelapsed
DEFAULT_CIRC_SEQS0.010.000.01
FeatureDb-class0.060.020.08
TranscriptDb-class1.300.111.42
as-format-methods2.360.002.36
extractTranscriptsFromGenome112.78 9.83122.62
features0.110.010.12
getPromoterSeq-methods3.790.224.01
id2name0.110.020.13
makeFeatureDbFromUCSC13.46 0.2888.22
makeTranscriptDb0.110.000.11
makeTranscriptDbFromBiomart 3.31 0.0125.54
makeTranscriptDbFromGFF2.650.082.73
makeTranscriptDbFromUCSC 7.27 0.0247.33
makeTxDbPackage0.460.030.49
nearest-methods1.700.031.73
saveFeatures000
select-methods0.250.000.25
transcripts3.950.023.96
transcriptsBy2.600.002.61
transcriptsByOverlaps0.640.000.63