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This page was generated on 2021-10-14 12:05:36 -0400 (Thu, 14 Oct 2021).

CHECK results for icetea on riesling1

To the developers/maintainers of the icetea package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/icetea.git to
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raw results

Package 890/2056HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
icetea 1.11.0  (landing page)
Vivek Bhardwaj
Snapshot Date: 2021-10-13 14:50:09 -0400 (Wed, 13 Oct 2021)
git_url: https://git.bioconductor.org/packages/icetea
git_branch: master
git_last_commit: 61ed70e
git_last_commit_date: 2021-05-19 12:36:20 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: icetea
Version: 1.11.0
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings icetea_1.11.0.tar.gz
StartedAt: 2021-10-14 01:32:35 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 01:40:22 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 466.2 seconds
RetCode: 0
Status:   OK  
CheckDir: icetea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings icetea_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/icetea.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 'icetea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'icetea' version '1.11.0'
* 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 'icetea' 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 ... NOTE
detectTSS,CapSet : <anonymous>: no visible binding for global variable
  'logFC'
fitDiffTSS,CapSet: no visible binding for global variable 'ResizeReads'
Undefined global functions or variables:
  ResizeReads logFC
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
detectTSS      11.64   0.96   21.66
annotateTSS     6.78   0.19    6.97
getNormFactors  1.24   0.02   14.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
detectTSS      11.58   0.81   21.76
annotateTSS     6.30   0.20    6.50
getNormFactors  1.34   0.05   20.48
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/icetea.Rcheck/00check.log'
for details.



Installation output

icetea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/icetea_1.11.0.tar.gz && rm -rf icetea.buildbin-libdir && mkdir icetea.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=icetea.buildbin-libdir icetea_1.11.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL icetea_1.11.0.zip && rm icetea_1.11.0.tar.gz icetea_1.11.0.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
 65 1305k   65  848k    0     0  2263k      0 --:--:-- --:--:-- --:--:-- 2263k
100 1305k  100 1305k    0     0  2692k      0 --:--:-- --:--:-- --:--:-- 2687k

install for i386

* installing *source* package 'icetea' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'icetea'
    finding HTML links ... done
    activeChrs                              html  
    annotateTSS                             html  
    check_capSet                            html  
    demultiplexFASTQ                        html  
    detectDiffTSS                           html  
    finding level-2 HTML links ... done

    detectTSS                               html  
    diffQCplots                             html  
    exampleCSobject                         html  
    exportTSS                               html  
    filterDuplicates                        html  
    filterDups                              html  
    fitDiffTSS                              html  
    getBamFlags                             html  
    getChromBins                            html  
    getChromWindows                         html  
    getGeneCounts                           html  
    getMCparams                             html  
    getNormFactors                          html  
    get_newfastq                            html  
    getranks                                html  
    mapCaps                                 html  
    newCapSet                               html  
    numReadsInBed                           html  
    plotPrecision                           html  
    plotReadStats                           html  
    plotTSSprecision                        html  
    readsTo3p                               html  
    readsTo5p                               html  
    readsToCenter                           html  
    sampleInfo                              html  
    splitBAM_byIndex                        html  
    splitBAM_byRepindex                     html  
    split_fastq                             html  
    splitranks                              html  
    strandBinCounts                         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 'icetea' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'icetea' as icetea_1.11.0.zip
* DONE (icetea)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'icetea' successfully unpacked and MD5 sums checked

Tests output

icetea.Rcheck/tests_i386/testthat.Rout


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(icetea)
> 
> test_check("icetea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  26.73    1.18   42.60 

icetea.Rcheck/tests_x64/testthat.Rout


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(icetea)
> 
> test_check("icetea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  28.09    1.37   44.59 

Example timings

icetea.Rcheck/examples_i386/icetea-Ex.timings

nameusersystemelapsed
annotateTSS6.780.196.97
demultiplexFASTQ1.120.051.18
detectDiffTSS000
detectTSS11.64 0.9621.66
exampleCSobject0.040.000.05
exportTSS0.130.000.12
filterDuplicates0.870.060.94
fitDiffTSS000
getGeneCounts1.160.031.19
getNormFactors 1.24 0.0214.78
mapCaps000
newCapSet0.030.000.03
plotReadStats0.180.000.19
plotTSSprecision1.410.051.45
sampleInfo0.060.000.06
splitBAM_byIndex0.150.060.22
splitBAM_byRepindex0.160.060.22

icetea.Rcheck/examples_x64/icetea-Ex.timings

nameusersystemelapsed
annotateTSS6.30.26.5
demultiplexFASTQ1.930.051.99
detectDiffTSS000
detectTSS11.58 0.8121.76
exampleCSobject0.050.010.07
exportTSS0.120.000.12
filterDuplicates0.910.070.99
fitDiffTSS000
getGeneCounts1.220.011.23
getNormFactors 1.34 0.0520.48
mapCaps000
newCapSet0.050.000.05
plotReadStats0.20.00.2
plotTSSprecision1.390.051.44
sampleInfo0.050.010.06
splitBAM_byIndex0.230.060.32
splitBAM_byRepindex0.210.070.26