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Package 87/479HostnameOS / ArchBUILDCHECKBUILD BIN
ChIPpeakAnno 1.9.5
Lihua Julie Zhu
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 56501 / Revision: 56603
Last Changed Date: 2011-07-01 14:01:35 -0700 (Fri, 01 Jul 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ChIPpeakAnno
Version: 1.9.5
Command: mkdir ChIPpeakAnno.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_1.9.5.tar.gz >ChIPpeakAnno-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_1.9.5.tar.gz && mv ChIPpeakAnno.buildbin-libdir/* ChIPpeakAnno.Rcheck/ && rmdir ChIPpeakAnno.buildbin-libdir
StartedAt: 2011-07-07 04:32:32 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:39:23 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 411.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* 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 '1.9.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ChIPpeakAnno' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.5Mb
  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
* 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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:28-29: Dropping empty section \details
prepare_Rd: annotatePeakInBatch.Rd:45-46: 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:53-55: 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:17-19: Dropping empty section \details
prepare_Rd: getAnnotation.Rd:31: Dropping empty section \seealso
prepare_Rd: getEnrichedGO.Rd:22-23: Dropping empty section \details
prepare_Rd: getEnrichedGO.Rd:92-95: 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:45-47: Dropping empty section \note
prepare_Rd: makeVennDiagram.Rd:40-41: 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                               old_size new_size compress
  ExonPlusUtr.human.GRCh37.rda    8.6Mb    4.2Mb       xz
  TSS.human.GRCh37.rda            1.1Mb    624Kb       xz
  TSS.human.NCBI36.rda            1.1Mb    693Kb       xz
  TSS.mouse.NCBIM37.rda           1.0Mb    610Kb       xz
  TSS.rat.RGSC3.4.rda             772Kb    463Kb       xz
  TSS.zebrafish.Zv8.rda           706Kb    413Kb       xz
  annotatedPeak.rda               540Kb    297Kb       xz
  myPeakList.rda                  173Kb     75Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

ChIPpeakAnno.Rcheck/00install.out:


install for i386

* installing *source* package 'ChIPpeakAnno' ...
** R
** data
** inst
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'ChIPpeakAnno.Rnw' 
** testing if installed package can be loaded
Warning messages:
1: replacing previous import 'space' when loading 'IRanges' 
2: replacing previous import 'getSeq' when loading 'BSgenome' 

add DLL for x64

* installing *source* package 'ChIPpeakAnno' ...
** testing if installed package can be loaded
Warning messages:
1: replacing previous import 'space' when loading 'IRanges' 
2: replacing previous import 'getSeq' when loading 'BSgenome' 
* MD5 sums
packaged installation of 'ChIPpeakAnno' as ChIPpeakAnno_1.9.5.zip

* DONE (ChIPpeakAnno)

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.040.000.03
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh375.660.025.68
GFF2RangedData0.010.000.02
Peaks.Ste12.Replicate10.040.000.03
Peaks.Ste12.Replicate20.030.000.03
Peaks.Ste12.Replicate30.030.000.03
TSS.human.GRCh370.150.000.16
TSS.human.NCBI360.380.020.39
TSS.mouse.NCBIM370.110.000.11
TSS.rat.RGSC3.40.090.000.09
TSS.zebrafish.Zv80.080.000.08
addAncestors2.730.042.78
annotatePeakInBatch0.010.000.02
annotatedPeak0.110.000.11
convert2EntrezID0.370.000.37
enrichedGO000
findOverlappingPeaks0.020.000.02
getAllPeakSequence0.520.030.54
getAnnotation000
getEnrichedGO0.020.000.01
getGeneSeq000
getUniqueGOidCount000
hyperGtest000
makeVennDiagram000
myPeakList0.020.000.01
write2FASTA0.060.000.07