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CHECK report for RNAdecay on tokay2

This page was generated on 2019-10-16 12:41:21 -0400 (Wed, 16 Oct 2019).

Package 1393/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAdecay 1.4.0
Reed Sorenson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RNAdecay
Branch: RELEASE_3_9
Last Commit: 993968e
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 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 ] ERROR 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAdecay
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAdecay.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RNAdecay_1.4.0.tar.gz
StartedAt: 2019-10-16 06:42:17 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:45:33 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 196.1 seconds
RetCode: 0
Status:  OK  
CheckDir: RNAdecay.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:RNAdecay.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RNAdecay_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RNAdecay.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 'RNAdecay/DESCRIPTION' ... OK
* this is package 'RNAdecay' version '1.4.0'
* 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 'RNAdecay' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 154.0Mb
  sub-directories of 1Mb or more:
    data    2.7Mb
    libs  151.1Mb
* 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
decay_plot: no visible binding for global variable 'text'
decay_plot: no visible binding for global variable 'x'
decay_plot: no visible binding for global variable 'y'
decay_plot: no visible binding for global variable 't.decay'
decay_plot: no visible binding for global variable 'value'
decay_plot: no visible binding for global variable 'treatment'
Undefined global functions or variables:
  t.decay text treatment value x y
Consider adding
  importFrom("graphics", "text")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... 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/RNAdecay/libs/i386/general_Exp_1sse.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/RNAdecay/libs/x64/general_Exp_1sse.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/RNAdecay/libs/i386/general_Exp_2sse.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/RNAdecay/libs/x64/general_Exp_2sse.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/RNAdecay/libs/i386/general_Exp_3sse.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/RNAdecay/libs/x64/general_Exp_3sse.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/RNAdecay/libs/i386/general_Exp_4sse.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/RNAdecay/libs/x64/general_Exp_4sse.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/RNAdecay/libs/i386/general_dExp_1sse.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/RNAdecay/libs/x64/general_dExp_1sse.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/RNAdecay/libs/i386/general_dExp_2sse.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/RNAdecay/libs/x64/general_dExp_2sse.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/RNAdecay/libs/i386/general_dExp_3sse.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/RNAdecay/libs/x64/general_dExp_3sse.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/RNAdecay/libs/i386/general_dExp_4sse.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/RNAdecay/libs/x64/general_dExp_4sse.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
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/RNAdecay.Rcheck/00check.log'
for details.



Installation output

RNAdecay.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/RNAdecay_1.4.0.tar.gz && rm -rf RNAdecay.buildbin-libdir && mkdir RNAdecay.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAdecay.buildbin-libdir RNAdecay_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RNAdecay_1.4.0.zip && rm RNAdecay_1.4.0.tar.gz RNAdecay_1.4.0.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
100 2724k  100 2724k    0     0  23.6M      0 --:--:-- --:--:-- --:--:-- 25.3M

install for i386

* installing *source* package 'RNAdecay' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_1sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_1sse.cpp -o general_dExp_1sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_dExp_1sse.dll tmp.def general_dExp_1sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_1sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_1sse.cpp -o general_Exp_1sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_Exp_1sse.dll tmp.def general_Exp_1sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_2sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_2sse.cpp -o general_dExp_2sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_dExp_2sse.dll tmp.def general_dExp_2sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_2sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_2sse.cpp -o general_Exp_2sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_Exp_2sse.dll tmp.def general_Exp_2sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_3sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_3sse.cpp -o general_dExp_3sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_dExp_3sse.dll tmp.def general_dExp_3sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_3sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_3sse.cpp -o general_Exp_3sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_Exp_3sse.dll tmp.def general_Exp_3sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_4sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_4sse.cpp -o general_dExp_4sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_dExp_4sse.dll tmp.def general_dExp_4sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_4sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_4sse.cpp -o general_Exp_4sse.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o general_Exp_4sse.dll tmp.def general_Exp_4sse.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
[1] 0
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/RNAdecay.buildbin-libdir/00LOCK-RNAdecay/00new/RNAdecay/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 'RNAdecay'
    finding HTML links ... done
    RPMs                                    html  
    a_high                                  html  
    aic                                     html  
    cols                                    html  
    comb_cv                                 html  
    const_decay                             html  
    constraint_fun_list_maker               html  
    decay_data                              html  
    decay_plot                              html  
    fit_var                                 html  
    group_map                               html  
    groupings                               html  
    log_lik                                 html  
    mod_optimization                        html  
    models                                  html  
    n_par                                   html  
    plain_theme                             html  
    results                                 html  
    sse_null_decaying_decay                 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 'RNAdecay' ...
** libs
  running 'src/Makefile.win' ...
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_1sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_1sse.cpp -o general_dExp_1sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_dExp_1sse.dll tmp.def general_dExp_1sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_1sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_1sse.cpp -o general_Exp_1sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_Exp_1sse.dll tmp.def general_Exp_1sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_2sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_2sse.cpp -o general_dExp_2sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_dExp_2sse.dll tmp.def general_dExp_2sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_2sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_2sse.cpp -o general_Exp_2sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_Exp_2sse.dll tmp.def general_Exp_2sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_3sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_3sse.cpp -o general_dExp_3sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_dExp_3sse.dll tmp.def general_dExp_3sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_3sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_3sse.cpp -o general_Exp_3sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_Exp_3sse.dll tmp.def general_Exp_3sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_dExp_4sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_dExp_4sse.cpp -o general_dExp_4sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_dExp_4sse.dll tmp.def general_dExp_4sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/TMB/include -IC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/RCPPEI~1/include     -DTMB_LIB_INIT=R_init_general_Exp_4sse     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_Exp_4sse.cpp -o general_Exp_4sse.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o general_Exp_4sse.dll tmp.def general_Exp_4sse.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
[1] 0
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/RNAdecay.buildbin-libdir/RNAdecay/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAdecay' as RNAdecay_1.4.0.zip
* DONE (RNAdecay)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RNAdecay' successfully unpacked and MD5 sums checked

Tests output


Example timings

RNAdecay.Rcheck/examples_i386/RNAdecay-Ex.timings

nameusersystemelapsed
a_high000
aic000
cols000
comb_cv000
const_decay000
constraint_fun_list_maker0.010.000.02
decay_plot1.280.111.40
fit_var000
group_map0.160.030.19
groupings000
log_lik000
mod_optimization2.090.032.75
n_par000
plain_theme0.100.000.09
sse_null_decaying_decay000

RNAdecay.Rcheck/examples_x64/RNAdecay-Ex.timings

nameusersystemelapsed
a_high000
aic000
cols000
comb_cv000
const_decay000
constraint_fun_list_maker000
decay_plot1.250.061.33
fit_var000
group_map0.140.000.14
groupings000
log_lik000
mod_optimization1.990.114.11
n_par000
plain_theme0.140.000.14
sse_null_decaying_decay000