Multiple platform build/check report for BioC 3.13 - CHECK results for PhosR on tokay2

Package: PhosR

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PhosR_1.2.0.tar.gz

StartedAt: 2021-10-15 03:24:37 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 03:29:31 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 294.0 seconds

RetCode: 0

Status: OK

CheckDir: PhosR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PhosR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PhosR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PhosR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PhosR' 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'PhosR' 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
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'S4Vectors:::disableValidity'
  'SummarizedExperiment:::.SummarizedExperiment.charbound'
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/PhosR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/PhosR_1.2.0.tar.gz && rm -rf PhosR.buildbin-libdir && mkdir PhosR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PhosR.buildbin-libdir PhosR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PhosR_1.2.0.zip && rm PhosR_1.2.0.tar.gz PhosR_1.2.0.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
 15 6100k   15  965k    0     0  1612k      0  0:00:03 --:--:--  0:00:03 1613k
 62 6100k   62 3823k    0     0  2392k      0  0:00:02  0:00:01  0:00:01 2392k
100 6100k  100 6100k    0     0  2736k      0  0:00:02  0:00:02 --:--:-- 2738k

install for i386

* installing *source* package 'PhosR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PhosR'
    finding HTML links ... done
    KinaseFamily                            html  
    PhosphoExperiment-methods               html  
    PhosphoExperiment-operate               html  
    finding level-2 HTML links ... done

    PhosphoExperiment                       html  
    PhosphoSite.human                       html  
    PhosphoSite.mouse                       html  
    PhosphoSite.rat                         html  
    RUVphospho                              html  
    SPSs                                    html  
    Signalomes                              html  
    createFrequencyMat                      html  
    frequencyScoring                        html  
    getSPS                                  html  
    hSEGs                                   html  
    kinaseSubstrateHeatmap                  html  
    kinaseSubstratePred                     html  
    kinaseSubstrateProfile                  html  
    kinaseSubstrateScore                    html  
    mIntersect                              html  
    mSEGs                                   html  
    matANOVA                                html  
    meanAbundance                           html  
    medianScaling                           html  
    minmax                                  html  
    motif.human.list                        html  
    motif.mouse.list                        html  
    motif.rat.list                          html  
    pathwayOverrepresent                    html  
    pathwayRankBasedEnrichment              html  
    phosCollapse                            html  
    phospho.L6.ratio                        html  
    phospho.L6.ratio.pe                     html  
    phospho.cells.Ins                       html  
    phospho.liver.Ins.TC.ratio.RUV          html  
    phospho.liver.Ins.TC.ratio.RUV.pe       html  
    plotKinaseNetwork                       html  
    plotQC                                  html  
    plotSignalomeMap                        html  
    ptImpute                                html  
    scImpute                                html  
    selectGrps                              html  
    selectLocalisedSites                    html  
    selectOverallPercent                    html  
    selectTimes                             html  
    siteAnnotate                            html  
    standardise                             html  
    tImpute                                 html  
*** copying figures
** 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 'PhosR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PhosR' as PhosR_1.2.0.zip
* DONE (PhosR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'PhosR' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(PhosR)
> 
> test_check("PhosR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
   7.42    0.64    8.04


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(PhosR)
> 
> test_check("PhosR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
   8.85    0.54    9.39

name	user	system	elapsed
PhosphoExperiment-methods	0.39	0.05	0.44
PhosphoExperiment-operate	1.07	0.01	1.08
PhosphoExperiment	0.40	0.05	0.45
RUVphospho	0.28	0.05	0.33
Signalomes	0	0	0
createFrequencyMat	0.14	0.00	0.16
frequencyScoring	0.49	0.04	0.53
getSPS	2.20	0.38	2.57
kinaseSubstrateHeatmap	0	0	0
kinaseSubstratePred	0	0	0
kinaseSubstrateProfile	0	0	0
kinaseSubstrateScore	0	0	0
mIntersect	1.06	0.03	1.10
matANOVA	0	0	0
meanAbundance	0.30	0.05	0.35
medianScaling	0.30	0.05	0.34
minmax	0	0	0
pathwayOverrepresent	0	0	0
pathwayRankBasedEnrichment	0	0	0
phosCollapse	0.95	0.05	1.00
plotQC	4.28	0.04	4.53
ptImpute	0.34	0.00	0.34
scImpute	1.25	0.00	1.25
selectGrps	0.19	0.02	0.21
selectLocalisedSites	0.14	0.00	0.14
selectOverallPercent	0.08	0.00	0.07
selectTimes	0.01	0.00	0.02
siteAnnotate	0	0	0
standardise	0	0	0
tImpute	0.25	0.01	0.27

name	user	system	elapsed
PhosphoExperiment-methods	0.35	0.00	0.34
PhosphoExperiment-operate	0.60	0.00	0.59
PhosphoExperiment	0.81	0.00	0.81
RUVphospho	0.21	0.01	0.22
Signalomes	0	0	0
createFrequencyMat	0.09	0.02	0.11
frequencyScoring	0.53	0.08	0.61
getSPS	1.86	0.08	1.94
kinaseSubstrateHeatmap	0	0	0
kinaseSubstratePred	0	0	0
kinaseSubstrateProfile	0	0	0
kinaseSubstrateScore	0	0	0
mIntersect	1.17	0.00	1.17
matANOVA	0	0	0
meanAbundance	0.26	0.04	0.32
medianScaling	0.32	0.02	0.32
minmax	0	0	0
pathwayOverrepresent	0	0	0
pathwayRankBasedEnrichment	0	0	0
phosCollapse	0.89	0.07	0.95
plotQC	4.87	0.04	4.92
ptImpute	0.27	0.02	0.29
scImpute	0.79	0.00	0.79
selectGrps	0.15	0.00	0.14
selectLocalisedSites	0.09	0.01	0.11
selectOverallPercent	0.05	0.00	0.05
selectTimes	0.01	0.00	0.02
siteAnnotate	0	0	0
standardise	0	0	0
tImpute	0.19	0.04	0.21

CHECK results for PhosR on tokay2

Summary

Command output

Installation output

Tests output

Example timings