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CHECK report for iCARE on tokay2

This page was generated on 2019-04-09 12:25:34 -0400 (Tue, 09 Apr 2019).

Package 772/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCARE 1.11.6
Bill Wheeler
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/iCARE
Branch: master
Last Commit: 01e086b
Last Changed Date: 2019-02-27 16:26:17 -0400 (Wed, 27 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: iCARE
Version: 1.11.6
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCARE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iCARE_1.11.6.tar.gz
StartedAt: 2019-04-09 03:33:46 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:38:23 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 277.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: iCARE.Rcheck
Warnings: 1

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:iCARE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iCARE_1.11.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/iCARE.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iCARE/DESCRIPTION' ... OK
* this is package 'iCARE' version '1.11.6'
* 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 'iCARE' 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 data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  bc_data.rda    1.2Mb    662Kb       xz
* 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/iCARE/libs/i386/iCARE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/iCARE/libs/x64/iCARE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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
compute.absolute.risk.split.interval 14.31   2.51   16.83
compute.absolute.risk                 8.35   1.13    9.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
compute.absolute.risk.split.interval 14.42   2.78   17.20
compute.absolute.risk                 9.69   1.36   11.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/iCARE.Rcheck/00check.log'
for details.



Installation output

iCARE.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/iCARE_1.11.6.tar.gz && rm -rf iCARE.buildbin-libdir && mkdir iCARE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iCARE.buildbin-libdir iCARE_1.11.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL iCARE_1.11.6.zip && rm iCARE_1.11.6.tar.gz iCARE_1.11.6.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 1115k  100 1115k    0     0  16.2M      0 --:--:-- --:--:-- --:--:-- 18.1M

install for i386

* installing *source* package 'iCARE' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c source.c -o source.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o iCARE.dll tmp.def source.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/iCARE.buildbin-libdir/00LOCK-iCARE/00new/iCARE/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 'iCARE'
    finding HTML links ... done
    bc_data                                 html  
    compute.absolute.risk                   html  
    compute.absolute.risk.split.interval    html  
    iCARE                                   html  
    model_validation                        html  
    plotModelValidation                     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 'iCARE' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c source.c -o source.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o iCARE.dll tmp.def source.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/iCARE.buildbin-libdir/iCARE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCARE' as iCARE_1.11.6.zip
* DONE (iCARE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'iCARE' successfully unpacked and MD5 sums checked

Tests output

iCARE.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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.

> BiocGenerics:::testPackage("iCARE")

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

   user  system elapsed 
   2.31    0.49    2.81 
   user  system elapsed 
   2.28    0.43    2.72 
   user  system elapsed 
   2.37    0.48    2.87 


RUNIT TEST PROTOCOL -- Tue Apr 09 03:37:48 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
iCARE RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  30.46    4.79   35.35 

iCARE.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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.

> BiocGenerics:::testPackage("iCARE")

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

   user  system elapsed 
   1.74    0.41    2.14 
   user  system elapsed 
   1.84    0.38    2.22 
   user  system elapsed 
   2.22    0.23    2.45 


RUNIT TEST PROTOCOL -- Tue Apr 09 03:38:18 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
iCARE RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  25.43    4.09   29.51 

Example timings

iCARE.Rcheck/examples_i386/iCARE-Ex.timings

nameusersystemelapsed
bc_data000
compute.absolute.risk8.351.139.50
compute.absolute.risk.split.interval14.31 2.5116.83
model_validation0.460.050.50
plotModelValidation0.450.120.58

iCARE.Rcheck/examples_x64/iCARE-Ex.timings

nameusersystemelapsed
bc_data000
compute.absolute.risk 9.69 1.3611.05
compute.absolute.risk.split.interval14.42 2.7817.20
model_validation0.370.060.44
plotModelValidation0.410.080.48