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BioC 3.2: CHECK report for fCI on moscato1

This page was generated on 2016-04-23 10:22:06 -0700 (Sat, 23 Apr 2016).

Package 338/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.0.0
Shaojun Tang
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/fCI
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: fCI
Version: 1.0.0
Command: rm -rf fCI.buildbin-libdir fCI.Rcheck && mkdir fCI.buildbin-libdir fCI.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fCI.buildbin-libdir fCI_1.0.0.tar.gz >fCI.Rcheck\00install.out 2>&1 && cp fCI.Rcheck\00install.out fCI-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=fCI.buildbin-libdir --install="check:fCI-install.out" --force-multiarch --no-vignettes --timings fCI_1.0.0.tar.gz
StartedAt: 2016-04-23 02:10:03 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:11:23 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 80.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: fCI.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf fCI.buildbin-libdir fCI.Rcheck && mkdir fCI.buildbin-libdir fCI.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fCI.buildbin-libdir fCI_1.0.0.tar.gz >fCI.Rcheck\00install.out 2>&1 && cp fCI.Rcheck\00install.out fCI-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=fCI.buildbin-libdir --install="check:fCI-install.out" --force-multiarch --no-vignettes --timings fCI_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/fCI.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fCI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fCI' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'FNN' 'psych' 'gtools' 'zoo' 'rgl' 'grid' 'VennDiagram'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'fCI' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'psych::logit' by 'gtools::logit' when loading 'fCI'
See 'D:/biocbld/bbs-3.2-bioc/meat/fCI.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  'NPCI'
Undocumented S4 methods:
  generic 'find.fci.targets' and siglist 'NPCI'
  generic 'show.targets' and siglist 'NPCI'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [5s] OK
** running examples for arch 'x64' ... [5s] 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
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/fCI.Rcheck/00check.log'
for details.


fCI.Rcheck/00install.out:


install for i386

* installing *source* package 'fCI' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'psych::logit' by 'gtools::logit' when loading 'fCI'
in method for 'initialize' with signature '"NPCI"': no definition for class "NPCI"
in method for 'normalization' with signature '"NPCI"': no definition for class "NPCI"
in method for 'populate' with signature '"NPCI"': no definition for class "NPCI"
in method for 'find.fci.targets' with signature '"NPCI"': no definition for class "NPCI"
in method for 'show.targets' with signature '"NPCI"': no definition for class "NPCI"
in method for 'call.npci' with signature '"NPCI"': no definition for class "NPCI"
in method for 'compute' with signature '"NPCI"': no definition for class "NPCI"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'psych::logit' by 'gtools::logit' when loading 'fCI'

install for x64

* installing *source* package 'fCI' ...
** testing if installed package can be loaded
Warning: replacing previous import 'psych::logit' by 'gtools::logit' when loading 'fCI'
* MD5 sums
packaged installation of 'fCI' as fCI_1.0.0.zip
* DONE (fCI)

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

nameusersystemelapsed
call.npci000
compute000
deg.pairwise.fold.change000
deg.up.down.info000
deseq.median.ratio.normalization000
divergence.multivariate.distributions000
fCI-class000
fCI.call.by.index1.140.141.28
figures000
find.fci.targets000
find.mid.point0.70.00.7
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.060.000.06
get.outline.index0.020.000.02
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists000
is.installed0.030.000.03
normalization000
npci.gene.by.pvalues0.010.000.02
npci.index.reconsidered0.080.000.08
npci.index.to.be.removed000
npci.venn.diagram0.430.001.55
pairwise.change.occupancy000
populate0.020.000.01
report.target.summary000
show.targets000
summarize0.010.000.02
total.library.size.normalization000
trim.size.normalization0.020.000.01
two.sample.log.ratio000
two.sample.permutation.test0.060.000.07
venndiagram000

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

nameusersystemelapsed
call.npci000
compute000
deg.pairwise.fold.change0.020.000.02
deg.up.down.info000
deseq.median.ratio.normalization0.010.000.01
divergence.multivariate.distributions0.020.000.02
fCI-class000
fCI.call.by.index1.530.191.71
figures000
find.fci.targets000
find.mid.point0.780.000.78
get.fold.large.step000
get.npci.data0.000.010.02
get.npci.distance.matrix0.030.000.03
get.outline.index0.010.000.02
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step0.020.000.01
intersect.of.lists000
is.installed0.020.000.02
normalization000
npci.gene.by.pvalues0.010.000.01
npci.index.reconsidered0.10.00.1
npci.index.to.be.removed000
npci.venn.diagram0.540.021.38
pairwise.change.occupancy000
populate0.020.000.02
report.target.summary000
show.targets000
summarize0.010.000.02
total.library.size.normalization000
trim.size.normalization0.020.000.01
two.sample.log.ratio000
two.sample.permutation.test0.040.000.05
venndiagram000