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CHECK report for CoreGx on tokay1

This page was generated on 2021-05-06 12:30:29 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CoreGx package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 379/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoreGx 1.2.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CoreGx
Branch: RELEASE_3_12
Last Commit: e2021c4
Last Changed Date: 2020-10-27 11:57:03 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CoreGx
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoreGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CoreGx_1.2.0.tar.gz
StartedAt: 2021-05-06 01:47:17 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:52:28 -0400 (Thu, 06 May 2021)
EllapsedTime: 311.2 seconds
RetCode: 0
Status:   OK   
CheckDir: CoreGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoreGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CoreGx_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CoreGx.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoreGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoreGx' version '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'CoreGx' 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 ... OK
* 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 ... 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 ... NOTE
  Note: found 8 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/CoreGx.Rcheck/00check.log'
for details.



Installation output

CoreGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CoreGx_1.2.0.tar.gz && rm -rf CoreGx.buildbin-libdir && mkdir CoreGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoreGx.buildbin-libdir CoreGx_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CoreGx_1.2.0.zip && rm CoreGx_1.2.0.tar.gz CoreGx_1.2.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1526k  100 1526k    0     0  15.1M      0 --:--:-- --:--:-- --:--:-- 15.2M

install for i386

* installing *source* package 'CoreGx' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'ggplot2':
  method        from
  print.element sets
Creating a generic function for 'colnames' from package 'base' in package 'CoreGx'
Creating a generic function for 'rownames' from package 'base' in package 'CoreGx'
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'colnames' from package 'base' in package 'CoreGx'
Creating a generic function for 'rownames' from package 'base' in package 'CoreGx'
** help
*** installing help indices
  converting help for package 'CoreGx'
    finding HTML links ... done
    CoreSet-class                           html  
    CoreSet                                 html  
    Create                                  html  
    LongTable-class                         html  
    LongTable                               html  
    RadioSet                                html  
    amcc                                    html  
    as                                      html  
    as.data.frame.LongTable                 html  
    as.data.table.LongTable                 html  
    as.long.table                           html  
    assayCols                               html  
    buildLongTable                          html  
    callingWaterfall                        html  
    cash-LongTable-method                   html  
    cellInfo-set                            html  
    cellInfo                                html  
    cellNames-set                           html  
    cellNames                               html  
    checkCsetStructure                      html  
    clevelandSmall_cSet                     html  
    colIDs                                  html  
    colMeta                                 html  
    connectivityScore                       html  
    cosinePerm                              html  
    curation-set                            html  
    curation                                html  
    datasetType-set                         html  
    datasetType                             html  
    dateCreated-set                         html  
    dateCreated                             html  
    dot-                                    html  
    dot-convertCSetMolecularProfilesToSE    html  
    dot-distancePointLine                   html  
    dot-distancePointSegment                html  
    dot-intersectList                       html  
    dot-symSetDiffList                      html  
    dot-unionList                           html  
    drugSensitivitySig                      html  
    fNames-set                              html  
    fNames                                  html  
    featureInfo-set                         html  
    featureInfo                             html  
    getIntern                               html  
    gwc                                     html  
    idCols-LongTable-method                 html  
    idCols                                  html  
    is.items                                html  
    list_or_LongTable-class                 html  
    mDataNames-set                          html  
    mDataNames                              html  
    mcc                                     html  
    merckLongTable                          html  
    metadata-LongTable-method               html  
    metadata-set-LongTable-method           html  
    molecularProfiles-set                   html  
    molecularProfiles                       html  
    molecularProfilesSlot-set               html  
    molecularProfilesSlot                   html  
    name-set                                html  
    name                                    html  
    pertNumber-set                          html  
    pertNumber                              html  
    phenoInfo-set                           html  
    phenoInfo                               html  
    reindex-LongTable-method                html  
    reindex                                 html  
    rowIDs                                  html  
    rowMeta                                 html  
    sensNumber-set                          html  
    sensNumber                              html  
    sensitivityInfo-set                     html  
    sensitivityInfo                         html  
    sensitivityMeasures-set                 html  
    sensitivityMeasures                     html  
    sensitivityProfiles-set                 html  
    sensitivityProfiles                     html  
    sensitivityRaw-set                      html  
    sensitivityRaw                          html  
    sensitivitySlot-set                     html  
    sensitivitySlot                         html  
    sensitivitySlotToLongTable              html  
    show-CoreSet-method                     html  
    show-LongTable-method                   html  
    showSigAnnot                            html  
    sub-LongTable-ANY-ANY-ANY-method        html  
    subset-LongTable-method                 html  
    subsetTo                                html  
    summarizeMolecularProfiles              html  
    summarizeSensitivityProfiles            html  
    updateCellId                            html  
** building package indices
** installing vignettes
** 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 'CoreGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoreGx' as CoreGx_1.2.0.zip
* DONE (CoreGx)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CoreGx' successfully unpacked and MD5 sums checked

Tests output

CoreGx.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CoreGx)
> 
> test_check("CoreGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
   8.85    0.92    9.75 

CoreGx.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CoreGx)
> 
> test_check("CoreGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
  13.56    0.48   14.03 

Example timings

CoreGx.Rcheck/examples_i386/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-class0.140.000.14
Create0.160.020.17
LongTable-class0.510.050.55
RadioSet000
amcc1.490.261.75
as0.110.030.13
as.data.frame.LongTable0.260.070.32
as.long.table0.060.030.09
assayCols000
buildLongTable000
callingWaterfall000
cash-LongTable-method0.020.000.01
cellInfo-set000
cellInfo000
cellNames-set0.220.020.23
cellNames000
checkCsetStructure0.050.000.05
colIDs000
colMeta000
connectivityScore0.090.010.11
cosinePerm0.060.000.06
curation0.010.000.01
datasetType-set0.020.000.02
datasetType0.010.000.02
dateCreated-set000
dateCreated000
dot-000
dot-distancePointLine000
dot-distancePointSegment000
dot-intersectList000
dot-symSetDiffList0.000.020.01
dot-unionList000
fNames-set0.040.000.03
fNames000
featureInfo-set0.010.000.02
featureInfo0.050.000.05
getIntern000
gwc0.080.060.14
idCols-LongTable-method000
idCols000
is.items000
mDataNames-set000
mDataNames000
mcc1.790.021.81
molecularProfiles-set0.050.000.05
molecularProfiles0.140.000.14
molecularProfilesSlot-set0.000.020.02
molecularProfilesSlot0.030.000.03
name-set000
name000
pertNumber-set000
pertNumber000
phenoInfo-set0.020.000.01
phenoInfo0.010.000.02
reindex000
rowIDs000
rowMeta000
sensNumber-set000
sensNumber000
sensitivityInfo-set000
sensitivityInfo000
sensitivityMeasures-set000
sensitivityMeasures000
sensitivityProfiles000
sensitivityRaw000
sensitivitySlot-set0.020.000.02
sensitivitySlot0.030.000.03
sensitivitySlotToLongTable000
show-CoreSet-method0.020.000.01
show-LongTable-method0.010.000.02
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.380.060.44
subset-LongTable-method0.220.060.28
summarizeMolecularProfiles0.010.000.01
summarizeSensitivityProfiles000
updateCellId0.050.000.05

CoreGx.Rcheck/examples_x64/CoreGx-Ex.timings

nameusersystemelapsed
CoreSet-class0.060.010.07
Create0.110.020.13
LongTable-class0.420.010.44
RadioSet000
amcc1.320.051.36
as0.060.000.06
as.data.frame.LongTable0.090.080.17
as.long.table0.050.000.05
assayCols000
buildLongTable000
callingWaterfall000
cash-LongTable-method0.010.000.01
cellInfo-set000
cellInfo000
cellNames-set0.130.000.13
cellNames000
checkCsetStructure0.030.000.03
colIDs000
colMeta000
connectivityScore0.060.000.06
cosinePerm0.050.000.05
curation0.020.000.01
datasetType-set0.010.000.02
datasetType0.020.000.01
dateCreated-set000
dateCreated000
dot-000
dot-distancePointLine000
dot-distancePointSegment000
dot-intersectList000
dot-symSetDiffList000
dot-unionList000
fNames-set0.030.000.03
fNames000
featureInfo-set000
featureInfo0.050.000.04
getIntern000
gwc0.120.010.14
idCols-LongTable-method000
idCols000
is.items000
mDataNames-set000
mDataNames000
mcc2.280.022.30
molecularProfiles-set0.060.020.08
molecularProfiles0.100.030.12
molecularProfilesSlot-set0.010.000.02
molecularProfilesSlot0.020.000.02
name-set000
name000
pertNumber-set000
pertNumber000
phenoInfo-set0.020.000.02
phenoInfo0.020.000.01
reindex000
rowIDs000
rowMeta000
sensNumber-set000
sensNumber000
sensitivityInfo-set000
sensitivityInfo000
sensitivityMeasures-set000
sensitivityMeasures000
sensitivityProfiles000
sensitivityRaw000
sensitivitySlot-set0.020.000.01
sensitivitySlot0.010.010.04
sensitivitySlotToLongTable000
show-CoreSet-method0.020.000.01
show-LongTable-method0.010.000.02
showSigAnnot000
sub-LongTable-ANY-ANY-ANY-method0.50.00.5
subset-LongTable-method0.300.020.31
summarizeMolecularProfiles000
summarizeSensitivityProfiles000
updateCellId0.060.000.06