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BioC 3.5: CHECK report for fCI on tokay2

This page was generated on 2017-10-18 14:24:56 -0400 (Wed, 18 Oct 2017).

Package 434/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.6.0
Shaojun Tang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/fCI
Branch: RELEASE_3_5
Last Commit: cad2176
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: fCI
Version: 1.6.0
Command: rm -rf fCI.buildbin-libdir fCI.Rcheck && mkdir fCI.buildbin-libdir fCI.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fCI.buildbin-libdir fCI_1.6.0.tar.gz >fCI.Rcheck\00install.out 2>&1 && cp fCI.Rcheck\00install.out fCI-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=fCI.buildbin-libdir --install="check:fCI-install.out" --force-multiarch --no-vignettes --timings fCI_1.6.0.tar.gz
StartedAt: 2017-10-17 23:43:38 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:44:53 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 75.8 seconds
RetCode: 0
Status:  OK  
CheckDir: fCI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf fCI.buildbin-libdir fCI.Rcheck && mkdir fCI.buildbin-libdir fCI.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fCI.buildbin-libdir fCI_1.6.0.tar.gz >fCI.Rcheck\00install.out 2>&1 && cp fCI.Rcheck\00install.out fCI-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=fCI.buildbin-libdir --install="check:fCI-install.out" --force-multiarch --no-vignettes --timings fCI_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/fCI.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.6.0'
* 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 ... 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
** 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 ... NOTE
fCI.call.by.index: no visible global function definition for 'new'
fCI.call.by.index: no visible global function definition for
  'initialize'
find.fci.targets,NPCI: no visible global function definition for
  'initialize'
populate,NPCI: no visible global function definition for '.hasSlot'
populate,NPCI: no visible global function definition for 'slot'
Undefined global functions or variables:
  .hasSlot initialize new slot
Consider adding
  importFrom("methods", ".hasSlot", "initialize", "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-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
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 'setfCI' 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

install for x64

* installing *source* package 'fCI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fCI' as fCI_1.6.0.zip
* DONE (fCI)

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

nameusersystemelapsed
NPCI-class000
call.npci000
compute000
deg.pairwise.fold.change000
deg.up.down.info000
deseq.median.ratio.normalization0.010.000.02
divergence.multivariate.distributions000
fCI-class000
fCI.call.by.index1.170.421.59
figures000
find.fci.targets2.820.012.83
find.mid.point0.480.000.48
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.030.000.03
get.outline.index000
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists000
is.installed0.010.000.02
normalization000
npci.gene.by.pvalues0.020.000.01
npci.index.reconsidered0.080.000.08
npci.index.to.be.removed000
npci.venn.diagram0.310.000.31
pairwise.change.occupancy000
populate000
report.target.summary000
setfCI000
show.targets000
summarize0.010.000.02
total.library.size.normalization000
trim.size.normalization000
two.sample.log.ratio000
two.sample.permutation.test0.040.000.03
venndiagram000

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

nameusersystemelapsed
NPCI-class000
call.npci000
compute000
deg.pairwise.fold.change000
deg.up.down.info000
deseq.median.ratio.normalization0.010.000.01
divergence.multivariate.distributions000
fCI-class000
fCI.call.by.index1.430.341.77
figures000
find.fci.targets3.180.053.23
find.mid.point0.60.00.6
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.030.000.04
get.outline.index0.020.000.01
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists000
is.installed0.020.000.02
normalization000
npci.gene.by.pvalues0.010.000.01
npci.index.reconsidered0.080.000.08
npci.index.to.be.removed000
npci.venn.diagram0.300.020.31
pairwise.change.occupancy000
populate000
report.target.summary000
setfCI000
show.targets000
summarize000
total.library.size.normalization0.010.000.02
trim.size.normalization000
two.sample.log.ratio000
two.sample.permutation.test0.030.000.03
venndiagram000