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CHECK report for fCI on tokay1

This page was generated on 2019-04-13 11:25:38 -0400 (Sat, 13 Apr 2019).

Package 511/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.12.0
Shaojun Tang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/fCI
Branch: RELEASE_3_8
Last Commit: 1d158e8
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: fCI
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fCI.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings fCI_1.12.0.tar.gz
StartedAt: 2019-04-13 02:12:04 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:14:05 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 121.0 seconds
RetCode: 0
Status:  OK  
CheckDir: fCI.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fCI.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings fCI_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/fCI.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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
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-3.8-bioc/meat/fCI.Rcheck/00check.log'
for details.



Installation output

fCI.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/fCI_1.12.0.tar.gz && rm -rf fCI.buildbin-libdir && mkdir fCI.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fCI.buildbin-libdir fCI_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL fCI_1.12.0.zip && rm fCI_1.12.0.tar.gz fCI_1.12.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  888k  100  888k    0     0  9660k      0 --:--:-- --:--:-- --:--:--  9.8M

install for i386

* installing *source* package 'fCI' ...
** R
** data
** inst
** byte-compile and prepare 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
  converting help for package 'fCI'
    finding HTML links ... done
    NPCI-class                              html  
    call.npci-methods                       html  
    call.npci                               html  
    compute-methods                         html  
    compute                                 html  
    deg.pairwise.fold.change                html  
    deg.up.down.info                        html  
    deseq.median.ratio.normalization        html  
    divergence.multivariate.distributions   html  
    fCI-class                               html  
    fCI.call.by.index                       html  
    fci.data                                html  
    figures-methods                         html  
    figures                                 html  
    find.fci.targets-methods                html  
    find.fci.targets                        html  
    find.mid.point                          html  
    get.fold.large.step                     html  
    get.npci.data                           html  
    get.npci.distance.matrix                html  
    get.outline.index                       html  
    get.protein.fold.step                   html  
    get.rank.combinations                   html  
    get.rna.fold.step                       html  
    initialize-methods                      html  
    intersect.of.lists                      html  
    is.installed                            html  
    multi.dimensional.fci.data              html  
    normalization-methods                   html  
    normalization                           html  
    npci.gene.by.pvalues                    html  
    npci.index.reconsidered                 html  
    npci.index.to.be.removed                html  
    npci.venn.diagram                       html  
    pairwise.change.occupancy               html  
    populate-methods                        html  
    populate                                html  
    report.target.summary                   html  
    setfCI-methods                          html  
    setfCI                                  html  
    show.targets-methods                    html  
    show.targets                            html  
    summarize-methods                       html  
    summarize                               html  
    total.library.size.normalization        html  
    trim.size.normalization                 html  
    two.sample.log.ratio                    html  
    two.sample.permutation.test             html  
    venndiagram-methods                     html  
    venndiagram                             html  
** building package indices
** installing vignettes
   'fCI.Rmd' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'fCI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fCI' as fCI_1.12.0.zip
* DONE (fCI)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'fCI' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

fCI.Rcheck/examples_i386/fCI-Ex.timings

nameusersystemelapsed
NPCI-class000
call.npci000
compute000
deg.pairwise.fold.change000
deg.up.down.info000
deseq.median.ratio.normalization000
divergence.multivariate.distributions0.010.000.01
fCI-class000
fCI.call.by.index1.420.602.02
figures000
find.fci.targets3.580.073.66
find.mid.point0.310.020.32
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.040.000.03
get.outline.index000
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists000
is.installed0.030.000.03
normalization000
npci.gene.by.pvalues000
npci.index.reconsidered0.130.000.12
npci.index.to.be.removed000
npci.venn.diagram0.150.010.17
pairwise.change.occupancy000
populate000
report.target.summary000
setfCI000
show.targets000
summarize0.020.000.02
total.library.size.normalization000
trim.size.normalization000
two.sample.log.ratio000
two.sample.permutation.test0.030.000.03
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.normalization000
divergence.multivariate.distributions0.020.000.02
fCI-class000
fCI.call.by.index1.480.592.07
figures000
find.fci.targets3.440.063.50
find.mid.point0.370.000.37
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.040.000.04
get.outline.index0.010.000.01
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists000
is.installed0.030.000.03
normalization000
npci.gene.by.pvalues000
npci.index.reconsidered0.130.000.13
npci.index.to.be.removed000
npci.venn.diagram0.150.000.15
pairwise.change.occupancy000
populate000
report.target.summary000
setfCI000
show.targets000
summarize000
total.library.size.normalization000
trim.size.normalization0.020.000.02
two.sample.log.ratio000
two.sample.permutation.test0.020.000.01
venndiagram000