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CHECK report for SPLINTER on tokay1

This page was generated on 2019-04-13 11:27:08 -0400 (Sat, 13 Apr 2019).

Package 1496/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.8.1
Diana Low
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/SPLINTER
Branch: RELEASE_3_8
Last Commit: c0320af
Last Changed Date: 2019-01-04 13:51:24 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SPLINTER
Version: 1.8.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPLINTER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SPLINTER_1.8.1.tar.gz
StartedAt: 2019-04-13 05:43:14 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:50:27 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 432.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SPLINTER.Rcheck
Warnings: 1

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:SPLINTER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SPLINTER_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SPLINTER.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 'SPLINTER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SPLINTER' version '1.8.1'
* package encoding: UTF-8
* 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'
 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 'SPLINTER' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SPLINTER.Rcheck/00install.out' for details.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
eventPlot   8.64   0.33    9.61
getPCRsizes 5.00   0.18    5.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
eventPlot            10.26   0.04   10.31
addEnsemblAnnotation  0.30   0.00    5.70
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/SPLINTER.Rcheck/00check.log'
for details.



Installation output

SPLINTER.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/SPLINTER_1.8.1.tar.gz && rm -rf SPLINTER.buildbin-libdir && mkdir SPLINTER.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SPLINTER.buildbin-libdir SPLINTER_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SPLINTER_1.8.1.zip && rm SPLINTER_1.8.1.tar.gz SPLINTER_1.8.1.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  803k   15  128k    0     0  2931k      0 --:--:-- --:--:-- --:--:-- 3121k
100  803k  100  803k    0     0  11.1M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'SPLINTER' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
** help
*** installing help indices
  converting help for package 'SPLINTER'
    finding HTML links ... done
    acceptor.m                              html  
    addEnsemblAnnotation                    html  
    annotateEvents                          html  
    callPrimer3                             html  
    checkPrimer                             html  
    compatible_cds                          html  
    compatible_tx                           html  
    donor.m                                 html  
    eventOutcomeCompare                     html  
    eventOutcomeTranslate                   html  
    eventPlot                               html  
    extendROI                               html  
    extractSpliceEvents                     html  
    extractSpliceSites                      html  
    findCompatibleEvents                    html  
    findCompatibleExon                      html  
    findExactOverlaps                       html  
    findTX                                  html  
    findTermination                         html  
    getPCRsizes                             html  
    getRegionDNA                            html  
    insertRegion                            html  
    makeROI                                 html  
    makeUniqueIDs                           html  
    matchExons                              html  
    metaremove                              html  
    pcr_result1                             html  
    plot_seqlogo                            html  
    primers                                 html  
    psiPlot                                 html  
    region_minus_exon                       html  
    removeRegion                            html  
    remvalue                                html  
    roi                                     html  
    shapiroAcceptor                         html  
    shapiroDensity                          html  
    shapiroDonor                            html  
    splice_data                             html  
    splice_fasta                            html  
    splitPCRhit                             html  
    thecds                                  html  
    theexons                                html  
    valid_cds                               html  
    valid_tx                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
In R CMD INSTALL

install for x64

* installing *source* package 'SPLINTER' ...
** testing if installed package can be loaded
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
* MD5 sums
packaged installation of 'SPLINTER' as SPLINTER_1.8.1.zip
* DONE (SPLINTER)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SPLINTER' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

SPLINTER.Rcheck/examples_i386/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m0.010.000.01
addEnsemblAnnotation0.300.123.07
callPrimer3000
checkPrimer0.120.050.17
compatible_cds000
compatible_tx000
donor.m000
eventOutcomeCompare1.120.201.33
eventOutcomeTranslate0.330.000.33
eventPlot8.640.339.61
extendROI0.490.000.48
extractSpliceEvents0.010.000.02
extractSpliceSites0.050.000.05
findCompatibleEvents0.220.000.22
findCompatibleExon0.170.000.17
findTX000
getPCRsizes5.000.185.19
getRegionDNA0.220.000.22
insertRegion0.090.000.10
makeROI0.210.000.21
makeUniqueIDs000
pcr_result1000
plot_seqlogo0.060.000.06
primers000
psiPlot0.260.020.28
region_minus_exon000
roi000
shapiroAcceptor0.360.010.42
shapiroDonor0.330.030.36
splice_data0.000.020.02
splice_fasta000
splitPCRhit000
thecds000
theexons000
valid_cds000
valid_tx000

SPLINTER.Rcheck/examples_x64/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m000
addEnsemblAnnotation0.30.05.7
callPrimer3000
checkPrimer0.130.000.12
compatible_cds0.000.010.02
compatible_tx000
donor.m000
eventOutcomeCompare1.170.051.22
eventOutcomeTranslate0.310.020.33
eventPlot10.26 0.0410.31
extendROI0.60.00.6
extractSpliceEvents000
extractSpliceSites0.060.000.06
findCompatibleEvents0.290.000.30
findCompatibleExon0.250.000.25
findTX000
getPCRsizes4.860.145.00
getRegionDNA0.220.020.24
insertRegion0.110.000.11
makeROI0.250.000.25
makeUniqueIDs000
pcr_result10.020.000.01
plot_seqlogo0.040.000.05
primers000
psiPlot0.240.000.23
region_minus_exon000
roi000
shapiroAcceptor0.350.020.36
shapiroDonor0.350.010.36
splice_data000
splice_fasta0.000.020.02
splitPCRhit000
thecds000
theexons000
valid_cds000
valid_tx0.010.000.01