Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:06:22 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for fCI on tokay2


To the developers/maintainers of the fCI package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fCI.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 630/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fCI 1.24.0  (landing page)
Shaojun Tang
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/fCI
git_branch: RELEASE_3_14
git_last_commit: 1dbe6dd
git_last_commit_date: 2021-10-26 12:21:13 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: fCI
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fCI.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings fCI_1.24.0.tar.gz
StartedAt: 2022-01-13 19:15:46 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 19:17:01 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 74.5 seconds
RetCode: 0
Status:   OK  
CheckDir: fCI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fCI.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings fCI_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/fCI.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.24.0'
* 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
* 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-3.14-bioc/meat/fCI.Rcheck/00check.log'
for details.



Installation output

fCI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/fCI_1.24.0.tar.gz && rm -rf fCI.buildbin-libdir && mkdir fCI.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fCI.buildbin-libdir fCI_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL fCI_1.24.0.zip && rm fCI_1.24.0.tar.gz fCI_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 77  884k   77  685k    0     0  2427k      0 --:--:-- --:--:-- --:--:-- 2430k
100  884k  100  884k    0     0  2854k      0 --:--:-- --:--:-- --:--:-- 2853k

install for i386

* installing *source* package 'fCI' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'fCI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fCI' as fCI_1.24.0.zip
* DONE (fCI)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'fCI' successfully unpacked and MD5 sums checked

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.distributions0.020.000.01
fCI-class000
fCI.call.by.index2.501.083.58
figures000
find.fci.targets4.870.044.92
find.mid.point0.270.000.26
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.020.000.02
get.outline.index000
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists000
is.installed0.040.000.05
normalization000
npci.gene.by.pvalues000
npci.index.reconsidered0.160.000.16
npci.index.to.be.removed000
npci.venn.diagram0.140.010.15
pairwise.change.occupancy000
populate000
report.target.summary000
setfCI000
show.targets000
summarize000
total.library.size.normalization0.000.020.02
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.distributions0.010.000.01
fCI-class0.000.020.02
fCI.call.by.index2.471.063.67
figures000
find.fci.targets4.710.034.74
find.mid.point0.280.000.28
get.fold.large.step000
get.npci.data000
get.npci.distance.matrix0.010.000.01
get.outline.index0.020.000.02
get.protein.fold.step000
get.rank.combinations000
get.rna.fold.step000
intersect.of.lists000
is.installed0.050.000.05
normalization000
npci.gene.by.pvalues000
npci.index.reconsidered0.140.000.14
npci.index.to.be.removed000
npci.venn.diagram0.140.020.15
pairwise.change.occupancy000
populate000
report.target.summary000
setfCI000
show.targets000
summarize000
total.library.size.normalization0.020.000.01
trim.size.normalization000
two.sample.log.ratio000
two.sample.permutation.test0.040.000.05
venndiagram000