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CHECK report for ToPASeq on tokay2

This page was generated on 2019-10-16 12:31:44 -0400 (Wed, 16 Oct 2019).

Package 1657/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ToPASeq 1.18.1
Ivana Ihnatova
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ToPASeq
Branch: RELEASE_3_9
Last Commit: 670936c
Last Changed Date: 2019-09-09 08:59:00 -0400 (Mon, 09 Sep 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ToPASeq
Version: 1.18.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ToPASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ToPASeq_1.18.1.tar.gz
StartedAt: 2019-10-16 07:35:39 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:50:23 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 884.1 seconds
RetCode: 0
Status:  OK  
CheckDir: ToPASeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ToPASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ToPASeq_1.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ToPASeq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ToPASeq/DESCRIPTION' ... OK
* this is package 'ToPASeq' version '1.18.1'
* 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 'ToPASeq' 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 R/sysdata.rda ... 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-3.9-bioc/R/library/ToPASeq/libs/i386/ToPASeq.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-3.9-bioc/R/library/ToPASeq/libs/x64/ToPASeq.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 or elapsed time > 5s
                            user system elapsed
CePa                       51.08  18.97   73.20
PRS                        50.88   2.48   55.78
PRS_wrapper                50.47   0.41   54.84
TAPPA                      50.16   0.25   50.43
SPIA                       44.25   0.15   45.47
DEGraph                    41.02   0.83   41.86
convertIdentifiersByVector 32.17   0.04   32.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
CePa                       43.34   0.84   45.13
TAPPA                      41.17   0.10   41.30
SPIA                       39.16   0.19   39.73
DEGraph                    38.30   0.31   38.70
PRS_wrapper                36.37   0.17   36.55
PRS                        36.13   0.29   37.29
convertIdentifiersByVector 35.42   0.00   35.77
* 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-3.9-bioc/meat/ToPASeq.Rcheck/00check.log'
for details.



Installation output

ToPASeq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ToPASeq_1.18.1.tar.gz && rm -rf ToPASeq.buildbin-libdir && mkdir ToPASeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ToPASeq.buildbin-libdir ToPASeq_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ToPASeq_1.18.1.zip && rm ToPASeq_1.18.1.tar.gz ToPASeq_1.18.1.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
100 47675  100 47675    0     0   778k      0 --:--:-- --:--:-- --:--:--  878k

install for i386

* installing *source* package 'ToPASeq' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c accCpp.cpp -o accCpp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c betweeness.cpp -o betweeness.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c colMinMax.cpp -o colMinMax.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c downstream.cpp -o downstream.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ToPASeq.dll tmp.def RcppExports.o accCpp.o betweeness.o colMinMax.o downstream.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ToPASeq.buildbin-libdir/00LOCK-ToPASeq/00new/ToPASeq/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ToPASeq'
    finding HTML links ... done
    CePa                                    html  
    DEGraph                                 html  
    PRS                                     html  
    finding level-2 HTML links ... done

    PRS_wrapper                             html  
    PWEA                                    html  
    SPIA                                    html  
    TAPPA                                   html  
    TopologyGSA                             html  
    clipper                                 html  
    convertIdentifiersByVector              html  
    res                                     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 'ToPASeq' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c accCpp.cpp -o accCpp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c betweeness.cpp -o betweeness.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c colMinMax.cpp -o colMinMax.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c downstream.cpp -o downstream.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ToPASeq.dll tmp.def RcppExports.o accCpp.o betweeness.o colMinMax.o downstream.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ToPASeq.buildbin-libdir/ToPASeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ToPASeq' as ToPASeq_1.18.1.zip
* DONE (ToPASeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ToPASeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

ToPASeq.Rcheck/examples_i386/ToPASeq-Ex.timings

nameusersystemelapsed
CePa51.0818.9773.20
DEGraph41.02 0.8341.86
PRS50.88 2.4855.78
PRS_wrapper50.47 0.4154.84
PWEA000
SPIA44.25 0.1545.47
TAPPA50.16 0.2550.43
TopologyGSA000
clipper000
convertIdentifiersByVector32.17 0.0432.40

ToPASeq.Rcheck/examples_x64/ToPASeq-Ex.timings

nameusersystemelapsed
CePa43.34 0.8445.13
DEGraph38.30 0.3138.70
PRS36.13 0.2937.29
PRS_wrapper36.37 0.1736.55
PWEA000
SPIA39.16 0.1939.73
TAPPA41.17 0.1041.30
TopologyGSA000
clipper000
convertIdentifiersByVector35.42 0.0035.77