Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 94/658HostnameOS / ArchBUILDCHECKBUILD BIN
CAGEr 0.99.1
Vanja Haberle
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAGEr
Last Changed Rev: 74273 / Revision: 74774
Last Changed Date: 2013-03-13 06:31:35 -0700 (Wed, 13 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CAGEr
Version: 0.99.1
Command: rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_0.99.1.tar.gz >CAGEr-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_0.99.1.tar.gz && mv CAGEr.buildbin-libdir/* CAGEr.Rcheck/ && rmdir CAGEr.buildbin-libdir
StartedAt: 2013-03-25 01:24:13 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:29:15 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 302.4 seconds
RetCode: 0
Status:  OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/CAGEr.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '0.99.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 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 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 ... NOTE
.cluster.ctss.strand: no visible binding for global variable 'tpm'
.ctss2clusters : <anonymous>: no visible binding for global variable
  'chr'
.ctss2clusters.predef : <anonymous>: no visible binding for global
  variable 'chr'
.distclu: no visible binding for global variable 'tpm'
.fit.power.law.to.reverse.cumulative: no visible binding for global
  variable 'nr_tags'
.getCumsum : <anonymous>: no visible binding for global variable 'chr'
.getCumsumChr2: no visible binding for global variable 'chr'
.make.consensus.clusters: no visible binding for global variable 'tpm'
.paraclu: no visible binding for global variable 'tpm'
.paraclu3 : <anonymous>: no visible binding for global variable 'chr'
.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'
.predefined.clusters: no visible binding for global variable 'tpm'
.summarize.clusters : <anonymous>: no visible binding for global
  variable 'cluster'
.summarize.clusters: no visible binding for global variable 'nr_ctss'
.summarize.clusters: no visible binding for global variable 'tpm'
.summarize.clusters.predef : <anonymous>: no visible binding for global
  variable 'cluster'
cumulativeCTSSdistribution,CAGEset: no visible binding for global
  variable 'tpm'
extractExpressionClass,CAGEset: no visible binding for global variable
  'expression_class'
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'
scoreShift,CAGEset-character-character : <anonymous>: no visible
  binding for global variable 'consensus.cluster'
* 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' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [40s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
importPublicData 15.21   0.23   15.51
** running examples for arch 'x64' ... [49s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
importPublicData  19.14   0.35   19.51
quantilePositions  5.65   0.00    5.65
* 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-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
   'CAGEr.Rnw' 
** 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_0.99.1.zip
* DONE (CAGEr)