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This page was generated on 2022-04-13 12:07:13 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 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 RiboDiPA on tokay2


To the developers/maintainers of the RiboDiPA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RiboDiPA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1605/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RiboDiPA 1.2.0  (landing page)
Ji-Ping Wang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/RiboDiPA
git_branch: RELEASE_3_14
git_last_commit: 0b22a63
git_last_commit_date: 2021-10-26 13:06:31 -0400 (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: RiboDiPA
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RiboDiPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RiboDiPA_1.2.0.tar.gz
StartedAt: 2022-04-13 01:42:31 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:55:30 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 779.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RiboDiPA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RiboDiPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RiboDiPA_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RiboDiPA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RiboDiPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RiboDiPA' 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 'RiboDiPA' 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RiboDiPA/libs/i386/RiboDiPA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RiboDiPA/libs/x64/RiboDiPA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
PsiteMapping        24.04   0.58   96.36
diffPatternTestExon  6.87   0.07    6.93
data.binned          5.72   0.08    5.79
DataBinning          2.73   0.94   60.41
data.psite           0.91   0.19   29.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
PsiteMapping        26.72   0.26  100.05
diffPatternTestExon  7.11   0.03    7.14
data.binned          6.10   0.00    6.10
DataBinning          2.81   0.43   58.23
data.psite           0.93   0.14   27.90
* 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-3.14-bioc/meat/RiboDiPA.Rcheck/00check.log'
for details.



Installation output

RiboDiPA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RiboDiPA_1.2.0.tar.gz && rm -rf RiboDiPA.buildbin-libdir && mkdir RiboDiPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RiboDiPA.buildbin-libdir RiboDiPA_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RiboDiPA_1.2.0.zip && rm RiboDiPA_1.2.0.tar.gz RiboDiPA_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
 69  245k   69  169k    0     0   501k      0 --:--:-- --:--:-- --:--:--  501k
100  245k  100  245k    0     0   352k      0 --:--:-- --:--:-- --:--:--  352k

install for i386

* installing *source* package 'RiboDiPA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c centerCPP.cpp -o centerCPP.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o RiboDiPA.dll tmp.def RcppExports.o centerCPP.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RiboDiPA.buildbin-libdir/00LOCK-RiboDiPA/00new/RiboDiPA/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RiboDiPA'
    finding HTML links ... done
    DataBinning                             html  
    PsiteMapping                            html  
    RiboDiPA                                html  
    data.binned                             html  
    data.psite                              html  
    diffPatternTest                         html  
    diffPatternTestExon                     html  
    normFactor                              html  
    plotTest                                html  
    plotTrack                               html  
    psitecal                                html  
    result.pst                              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 'RiboDiPA' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c centerCPP.cpp -o centerCPP.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o RiboDiPA.dll tmp.def RcppExports.o centerCPP.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RiboDiPA.buildbin-libdir/RiboDiPA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RiboDiPA' as RiboDiPA_1.2.0.zip
* DONE (RiboDiPA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RiboDiPA' successfully unpacked and MD5 sums checked

Tests output


Example timings

RiboDiPA.Rcheck/examples_i386/RiboDiPA-Ex.timings

nameusersystemelapsed
DataBinning 2.73 0.9460.41
PsiteMapping24.04 0.5896.36
RiboDiPA000
data.binned5.720.085.79
data.psite 0.91 0.1929.03
diffPatternTest4.770.014.79
diffPatternTestExon6.870.076.93
normFactor000
plotTest0.920.030.96
plotTrack2.710.032.73
psitecal000
result.pst2.840.032.88

RiboDiPA.Rcheck/examples_x64/RiboDiPA-Ex.timings

nameusersystemelapsed
DataBinning 2.81 0.4358.23
PsiteMapping 26.72 0.26100.05
RiboDiPA000
data.binned6.10.06.1
data.psite 0.93 0.1427.90
diffPatternTest4.880.004.88
diffPatternTestExon7.110.037.14
normFactor000
plotTest0.950.051.00
plotTrack2.970.002.97
psitecal000
result.pst3.060.003.06