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BioC 3.2: CHECK report for CAGEr on moscato1

This page was generated on 2015-08-20 13:21:25 -0700 (Thu, 20 Aug 2015).

Package 130/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.11.0
Vanja Haberle
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAGEr
Last Changed Rev: 102594 / Revision: 107602
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ ERROR ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.11.0
Command: rm -rf CAGEr.buildbin-libdir CAGEr.Rcheck && mkdir CAGEr.buildbin-libdir CAGEr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.11.0.tar.gz >CAGEr.Rcheck\00install.out 2>&1 && cp CAGEr.Rcheck\00install.out CAGEr-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.11.0.tar.gz
StartedAt: 2015-08-20 02:06:06 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 02:13:23 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 436.9 seconds
RetCode: 1
Status:  ERROR  
CheckDir: CAGEr.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CAGEr.buildbin-libdir CAGEr.Rcheck && mkdir CAGEr.buildbin-libdir CAGEr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.11.0.tar.gz >CAGEr.Rcheck\00install.out 2>&1 && cp CAGEr.Rcheck\00install.out CAGEr-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CAGEr.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.11.0'
* 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 'CAGEr' 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' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
.cluster.ctss.strand: no visible binding for global variable 'tpm'
.cluster.ctss.strand: no visible global function definition for 'Rle'
.ctss2clusters: no visible global function definition for 'detectCores'
.ctss2clusters: no visible global function definition for 'mclapply'
.ctss2clusters : <anonymous>: no visible binding for global variable
  'chr'
.ctss2clusters.predef: no visible global function definition for
  'detectCores'
.ctss2clusters.predef: no visible global function definition for
  'mclapply'
.ctss2clusters.predef : <anonymous>: no visible binding for global
  variable 'chr'
.distclu: no visible binding for global variable 'tpm'
.distclu: no visible global function definition for 'mclapply'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'removedG'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'pos'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'V1'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'V2'
.estimate.G.addition.and.correct: no visible binding for global
  variable 'nr_tags'
.fit.power.law.to.reverse.cumulative: no visible binding for global
  variable 'num'
.fit.power.law.to.reverse.cumulative: no visible binding for global
  variable 'nr_tags'
.get.quant.pos: no visible global function definition for 'detectCores'
.get.quant.pos: no visible global function definition for 'mclapply'
.getCumsum: no visible global function definition for 'detectCores'
.getCumsum: no visible global function definition for 'mclapply'
.getCumsum : <anonymous>: no visible binding for global variable 'chr'
.getCumsumChr: no visible global function definition for 'Rle'
.getCumsumChr2: no visible binding for global variable 'chr'
.getTotalTagCount: no visible binding for global variable 'tpm'
.getTotalTagCount: no visible binding for global variable
  'consensus.cluster'
.make.consensus.clusters: no visible binding for global variable 'tpm'
.paraclu: no visible binding for global variable 'tpm'
.paraclu3: no visible global function definition for 'detectCores'
.paraclu3 : <anonymous>: no visible binding for global variable 'chr'
.paraclu3: no visible global function definition for 'mclapply'
.paraclu3: no visible binding for global variable 'chr'
.paraclu3: no visible binding for global variable 'max_d'
.paraclu3: no visible binding for global variable 'min_d'
.paraclu3: no visible binding for global variable 'tpm'
.plotReverseCumulative: no visible binding for global variable 'num'
.plotReverseCumulative: no visible binding for global variable
  'nr_tags'
.predefined.clusters: no visible binding for global variable 'tpm'
.predefined.clusters: no visible global function definition for
  'mclapply'
.remove.added.G : <anonymous>: no visible binding for global variable
  'chr'
.remove.added.G: no visible binding for global variable 'removedG'
.remove.added.G: no visible binding for global variable 'chr'
.remove.added.G: no visible binding for global variable 'pos'
.remove.added.G: no visible binding for global variable 'nr_tags'
.remove.added.G: no visible binding for global variable 'tag_count'
.reverse.cumsum: no visible global function definition for
  'detectCores'
.reverse.cumsum: no visible global function definition for 'mclapply'
.score.promoter.shifting: no visible global function definition for
  'detectCores'
.score.promoter.shifting: no visible global function definition for
  'mclapply'
.summarize.clusters: no visible binding for global variable 'chr'
.summarize.clusters: no visible binding for global variable 'pos'
.summarize.clusters: no visible binding for global variable 'tpm'
.summarize.clusters: no visible binding for global variable 'cluster'
.summarize.clusters: no visible binding for global variable 'nr_ctss'
.summarize.clusters.predef: no visible binding for global variable
  'chr'
.summarize.clusters.predef: no visible binding for global variable
  'pos'
.summarize.clusters.predef: no visible binding for global variable
  'tpm'
.summarize.clusters.predef: no visible binding for global variable
  'cluster'
aggregateTagClusters,CAGEset: no visible binding for global variable
  'consensus.cluster'
aggregateTagClusters,CAGEset: no visible binding for global variable
  'chr'
aggregateTagClusters,CAGEset: no visible binding for global variable
  'tpm'
cumulativeCTSSdistribution,CAGEset: no visible binding for global
  variable 'tpm'
extractExpressionClass,CAGEset: no visible binding for global variable
  'expression_class'
getCTSS,CAGEset: no visible global function definition for 'seqlengths'
getCTSS,CAGEset: no visible binding for global variable 'tag_count'
getCTSS,CAGEset: no visible binding for global variable 'chr'
getCTSS,CAGEset: no visible binding for global variable 'pos'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'groupX.tpm'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'groupY.tpm'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'shifting.score'
getShiftingPromoters,CAGEset: no visible binding for global variable
  'fdr.KS'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ENCODEtissueCAGEfly'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ENCODEhumanCellLinesSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOMhumanSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOMmouseSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOM5humanSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'FANTOM5mouseSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ZebrafishSamples'
importPublicData,character-character-ANY-character: no visible binding
  for global variable 'ZebrafishCAGE'
scoreShift,CAGEset-character-character: no visible global function
  definition for 'detectCores'
scoreShift,CAGEset-character-character: no visible global function
  definition for 'mclapply'
scoreShift,CAGEset-character-character : <anonymous>: no visible
  binding for global variable 'consensus.cluster'
scoreShift,CAGEset-character-character : <anonymous> : <anonymous>: no
  visible global function definition for 'Rle'
scoreShift,CAGEset-character-character: no visible binding for global
  variable 'tagcount'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'CAGEr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: importPublicData
> ### Title: Importing publicly available CAGE data from various resources
> ### Aliases: importPublicData
> ###   importPublicData,character,character,ANY,character-method
> 
> ### ** Examples
> 
> ### importing FANTOM5 data
> 
> # list of FANTOM5 human tissue samples
> data(FANTOM5humanSamples)
> head(subset(FANTOM5humanSamples, type == "tissue"))
                          sample   type                  description library_id
959      achilles_tendon__donor2 tissue      achilles tendon, donor2  CNhs13435
840 adipose_tissue__adult__pool1 tissue adipose tissue, adult, pool1  CNhs10615
913  adrenal_gland__adult__pool1 tissue  adrenal gland, adult, pool1  CNhs11793
973 amygdala_-_adult__donor10196 tissue amygdala - adult, donor10196  CNhs13793
923  amygdala__adult__donor10252 tissue  amygdala, adult, donor10252  CNhs12311
885          aorta__adult__pool1 tissue          aorta, adult, pool1  CNhs11760
                                                                                                                                                          data_url
959              http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/achilles%2520tendon%252c%2520donor2.CNhs13435.10292-104G4.hg19.ctss.bed.gz
840 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adipose%2520tissue%252c%2520adult%252c%2520pool1.CNhs10615.10010-101C1.hg19.ctss.bed.gz
913  http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adrenal%2520gland%252c%2520adult%252c%2520pool1.CNhs11793.10081-102A9.hg19.ctss.bed.gz
973     http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/amygdala%2520-%2520adult%252c%2520donor10196.CNhs13793.10167-103B5.hg19.ctss.bed.gz
923      http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/amygdala%252c%2520adult%252c%2520donor10252.CNhs12311.10151-102I7.hg19.ctss.bed.gz
885              http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/aorta%252c%2520adult%252c%2520pool1.CNhs11760.10052-101G7.hg19.ctss.bed.gz
> 
> # import selected samples
> exampleCAGEset <- importPublicData(source="FANTOM5", dataset = "human", sample = c("adipose_tissue__adult__pool1", "adrenal_gland__adult__pool1", "aorta__adult__pool1"))
Fetching sample: adipose_tissue__adult__pool1...
Warning in scan(con, what = list(character(), NULL, integer(), NULL, integer(),  :
  InternetOpenUrl failed: 'The operation timed out'
Error in scan(con, what = list(character(), NULL, integer(), NULL, integer(),  : 
  cannot open the connection
Calls: importPublicData -> importPublicData -> scan
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'CAGEr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: importPublicData
> ### Title: Importing publicly available CAGE data from various resources
> ### Aliases: importPublicData
> ###   importPublicData,character,character,ANY,character-method
> 
> ### ** Examples
> 
> ### importing FANTOM5 data
> 
> # list of FANTOM5 human tissue samples
> data(FANTOM5humanSamples)
> head(subset(FANTOM5humanSamples, type == "tissue"))
                          sample   type                  description library_id
959      achilles_tendon__donor2 tissue      achilles tendon, donor2  CNhs13435
840 adipose_tissue__adult__pool1 tissue adipose tissue, adult, pool1  CNhs10615
913  adrenal_gland__adult__pool1 tissue  adrenal gland, adult, pool1  CNhs11793
973 amygdala_-_adult__donor10196 tissue amygdala - adult, donor10196  CNhs13793
923  amygdala__adult__donor10252 tissue  amygdala, adult, donor10252  CNhs12311
885          aorta__adult__pool1 tissue          aorta, adult, pool1  CNhs11760
                                                                                                                                                          data_url
959              http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/achilles%2520tendon%252c%2520donor2.CNhs13435.10292-104G4.hg19.ctss.bed.gz
840 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adipose%2520tissue%252c%2520adult%252c%2520pool1.CNhs10615.10010-101C1.hg19.ctss.bed.gz
913  http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adrenal%2520gland%252c%2520adult%252c%2520pool1.CNhs11793.10081-102A9.hg19.ctss.bed.gz
973     http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/amygdala%2520-%2520adult%252c%2520donor10196.CNhs13793.10167-103B5.hg19.ctss.bed.gz
923      http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/amygdala%252c%2520adult%252c%2520donor10252.CNhs12311.10151-102I7.hg19.ctss.bed.gz
885              http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/aorta%252c%2520adult%252c%2520pool1.CNhs11760.10052-101G7.hg19.ctss.bed.gz
> 
> # import selected samples
> exampleCAGEset <- importPublicData(source="FANTOM5", dataset = "human", sample = c("adipose_tissue__adult__pool1", "adrenal_gland__adult__pool1", "aorta__adult__pool1"))
Fetching sample: adipose_tissue__adult__pool1...
Warning in scan(con, what = list(character(), NULL, integer(), NULL, integer(),  :
  InternetOpenUrl failed: 'The operation timed out'
Error in scan(con, what = list(character(), NULL, integer(), NULL, integer(),  : 
  cannot open the connection
Calls: importPublicData -> importPublicData -> scan
Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/CAGEr.Rcheck/00check.log'
for details.

CAGEr.Rcheck/00install.out:


install for i386

* installing *source* package 'CAGEr' ...
** R
** data
** 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 'CAGEr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.11.0.zip
* DONE (CAGEr)

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

nameusersystemelapsed
CAGEset-class000
CTSSclusteringMethod0.050.000.04
CTSScoordinates0.060.000.07
CTSSnormalizedTpm0.090.000.09
CTSStagCount0.100.000.09
aggregateTagClusters0.930.010.97
clusterCTSS3.040.133.17
consensusClusters0.030.000.03
consensusClustersTpm0.030.000.04
cumulativeCTSSdistribution6.530.316.85
exportCTSStoBedGraph0.750.000.76
exportToBed0.990.000.99
expressionClasses0.070.000.07
extractExpressionClass0.080.000.08
genomeName0.030.000.03
getCTSS0.130.011.95
getExpressionProfiles1.180.001.19
getShiftingPromoters0.080.000.08

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

nameusersystemelapsed
CAGEset-class0.000.010.02
CTSSclusteringMethod0.030.000.03
CTSScoordinates0.050.000.04
CTSSnormalizedTpm0.080.000.08
CTSStagCount0.050.000.04
aggregateTagClusters1.140.001.16
clusterCTSS3.980.104.08
consensusClusters0.060.010.07
consensusClustersTpm0.050.000.05
cumulativeCTSSdistribution7.480.257.73
exportCTSStoBedGraph0.690.000.75
exportToBed1.010.021.03
expressionClasses0.050.000.05
extractExpressionClass0.060.000.06
genomeName0.050.000.05
getCTSS0.250.010.26
getExpressionProfiles1.070.001.12
getShiftingPromoters0.060.000.06