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Package 86/467HostnameOS / ArchBUILDCHECKBUILD BIN
ChIPpeakAnno 1.9.0
Lihua Julie Zhu
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 57838 / Revision: 59457
Last Changed Date: 2011-09-06 07:45:45 -0700 (Tue, 06 Sep 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: ChIPpeakAnno
Version: 1.9.0
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch ChIPpeakAnno_1.9.0.tar.gz
StartedAt: 2011-10-20 14:32:26 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:35:40 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 193.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '1.9.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ChIPpeakAnno' can be installed ... WARNING
Found the following significant warnings:
  Warning: LazyLoad = FALSE is deprecated
See 'E:/biocbld/bbs-2.8-bioc/meat/ChIPpeakAnno.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: BED2RangedData.Rd:15-17: Dropping empty section \details
prepare_Rd: BED2RangedData.Rd:22: Dropping empty section \references
prepare_Rd: BED2RangedData.Rd:27: Dropping empty section \seealso
prepare_Rd: ExonPlusUtr.human.GRCh37.Rd:28-30: Dropping empty section \source
prepare_Rd: ExonPlusUtr.human.GRCh37.Rd:31-32: Dropping empty section \references
prepare_Rd: GFF2RangedData.Rd:15-17: Dropping empty section \details
prepare_Rd: GFF2RangedData.Rd:22: Dropping empty section \references
prepare_Rd: GFF2RangedData.Rd:27: Dropping empty section \seealso
prepare_Rd: Peaks.Ste12.Replicate1.Rd:14-16: Dropping empty section \details
prepare_Rd: Peaks.Ste12.Replicate1.Rd:17-18: Dropping empty section \source
prepare_Rd: Peaks.Ste12.Replicate2.Rd:14-16: Dropping empty section \details
prepare_Rd: Peaks.Ste12.Replicate3.Rd:14-16: Dropping empty section \details
prepare_Rd: TSS.human.GRCh37.Rd:25-27: Dropping empty section \source
prepare_Rd: TSS.human.GRCh37.Rd:28-29: Dropping empty section \references
prepare_Rd: TSS.human.NCBI36.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.human.NCBI36.Rd:29-30: Dropping empty section \references
prepare_Rd: TSS.mouse.NCBIM37.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.mouse.NCBIM37.Rd:29-30: Dropping empty section \references
prepare_Rd: TSS.rat.RGSC3.4.Rd:25-27: Dropping empty section \source
prepare_Rd: TSS.rat.RGSC3.4.Rd:28-29: Dropping empty section \references
prepare_Rd: TSS.zebrafish.Zv8.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.zebrafish.Zv8.Rd:29-31: Dropping empty section \references
prepare_Rd: addAncestors.Rd:23-25: Dropping empty section \details
prepare_Rd: addAncestors.Rd:34-36: Dropping empty section \note
prepare_Rd: addAncestors.Rd:29-30: Dropping empty section \references
prepare_Rd: addAncestors.Rd:38-40: Dropping empty section \seealso
prepare_Rd: annotatePeakInBatch.Rd:25-26: Dropping empty section \details
prepare_Rd: annotatePeakInBatch.Rd:42-43: Dropping empty section \note
prepare_Rd: annotatedPeak.Rd:26-28: Dropping empty section \source
prepare_Rd: annotatedPeak.Rd:29-31: Dropping empty section \references
prepare_Rd: convert2EntrezID.Rd:20-22: Dropping empty section \details
prepare_Rd: convert2EntrezID.Rd:31-32: Dropping empty section \note
prepare_Rd: convert2EntrezID.Rd:26-27: Dropping empty section \references
prepare_Rd: convert2EntrezID.Rd:34-36: Dropping empty section \seealso
prepare_Rd: enrichedGO.Rd:79-81: Dropping empty section \details
prepare_Rd: enrichedGO.Rd:88-90: Dropping empty section \note
prepare_Rd: enrichedGO.Rd:82-83: Dropping empty section \source
prepare_Rd: enrichedGO.Rd:84-86: Dropping empty section \references
prepare_Rd: findOverlappingPeaks.Rd:48-50: Dropping empty section \note
prepare_Rd: findVennCounts.Rd:27-29: Dropping empty section \details
prepare_Rd: findVennCounts.Rd:35-37: Dropping empty section \references
prepare_Rd: findVennCounts.Rd:55-56: Dropping empty section \examples
prepare_Rd: getAllPeakSequence.Rd:20-22: Dropping empty section \details
prepare_Rd: getAllPeakSequence.Rd:31-34: Dropping empty section \note
prepare_Rd: getAllPeakSequence.Rd:35: Dropping empty section \seealso
prepare_Rd: getAnnotation.Rd:16-18: Dropping empty section \details
prepare_Rd: getAnnotation.Rd:30: Dropping empty section \seealso
prepare_Rd: getEnrichedGO.Rd:21-22: Dropping empty section \details
prepare_Rd: getEnrichedGO.Rd:91-94: Dropping empty section \note
prepare_Rd: getGeneSeq.Rd:15-17: Dropping empty section \details
prepare_Rd: getGeneSeq.Rd:26: Dropping empty section \references
prepare_Rd: getGeneSeq.Rd:31: Dropping empty section \seealso
prepare_Rd: getUniqueGOidCount.Rd:15-17: Dropping empty section \details
prepare_Rd: getUniqueGOidCount.Rd:23: Dropping empty section \references
prepare_Rd: makeVennDiagram.Rd:44-46: Dropping empty section \note
prepare_Rd: makeVennDiagram.Rd:39-40: Dropping empty section \references
prepare_Rd: myPeakList.Rd:14-15: Dropping empty section \details
prepare_Rd: myPeakList.Rd:19-20: Dropping empty section \references
prepare_Rd: write2FASTA.Rd:17-18: Dropping empty section \details
prepare_Rd: write2FASTA.Rd:24-26: Dropping empty section \note
prepare_Rd: write2FASTA.Rd:22: Dropping empty section \references
prepare_Rd: write2FASTA.Rd:27: Dropping empty section \seealso
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.8-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details

ChIPpeakAnno.Rcheck/00install.out:

* installing *source* package 'ChIPpeakAnno' ...
** R
** data
** inst
Warning: LazyLoad = FALSE is deprecated
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ChIPpeakAnno)

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.050.000.05
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh377.730.057.83
GFF2RangedData0.020.000.01
Peaks.Ste12.Replicate10.030.000.03
Peaks.Ste12.Replicate20.030.000.03
Peaks.Ste12.Replicate30.020.020.04
TSS.human.GRCh370.290.000.29
TSS.human.NCBI360.460.000.46
TSS.mouse.NCBIM370.140.000.14
TSS.rat.RGSC3.40.120.000.13
TSS.zebrafish.Zv80.110.000.11
addAncestors2.050.112.42
annotatePeakInBatch000
annotatedPeak0.140.000.14
convert2EntrezID0.390.000.44
enrichedGO000
findOverlappingPeaks000
getAllPeakSequence0.560.000.65
getAnnotation000
getEnrichedGO0.010.000.01
getGeneSeq000
getUniqueGOidCount000
hyperGtest0.020.000.02
makeVennDiagram000
myPeakList0.030.000.03
write2FASTA0.060.000.06