Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:08 -0400 (Fri, 15 Oct 2021).

CHECK results for iCARE on tokay2

To the developers/maintainers of the iCARE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iCARE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 891/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCARE 1.20.0  (landing page)
Bill Wheeler
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/iCARE
git_branch: RELEASE_3_13
git_last_commit: 9549cae
git_last_commit_date: 2021-05-19 12:17:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: iCARE
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCARE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings iCARE_1.20.0.tar.gz
StartedAt: 2021-10-15 00:34:04 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:37:53 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 229.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: iCARE.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCARE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings iCARE_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/iCARE.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 'iCARE/DESCRIPTION' ... OK
* this is package 'iCARE' version '1.20.0'
* 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 LazyData ... 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    668Kb       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-3.13-bioc/R/library/iCARE/libs/i386/iCARE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-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 (user + system) or elapsed time > 5s
                                      user system elapsed
compute.absolute.risk.split.interval 10.59   2.28   12.87
compute.absolute.risk                 6.04   1.19    7.23
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
compute.absolute.risk.split.interval 11.07   1.82   12.89
compute.absolute.risk                 7.25   0.99    8.23
* 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-3.13-bioc/meat/iCARE.Rcheck/00check.log'
for details.



Installation output

iCARE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/iCARE_1.20.0.tar.gz && rm -rf iCARE.buildbin-libdir && mkdir iCARE.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iCARE.buildbin-libdir iCARE_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL iCARE_1.20.0.zip && rm iCARE_1.20.0.tar.gz iCARE_1.20.0.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 1112k  100 1112k    0     0  1668k      0 --:--:-- --:--:-- --:--:-- 1670k

install for i386

* installing *source* package 'iCARE' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c source.c -o source.o
C:/rtools40/mingw32/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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c source.c -o source.o
C:/rtools40/mingw64/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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/iCARE.buildbin-libdir/iCARE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCARE' as iCARE_1.20.0.zip
* DONE (iCARE)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'iCARE' successfully unpacked and MD5 sums checked

Tests output

iCARE.Rcheck/tests_i386/runTests.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.

> BiocGenerics:::testPackage("iCARE")

Attaching package: 'Hmisc'

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

    format.pval, units

   user  system elapsed 
   1.27    0.36    1.63 
   user  system elapsed 
   1.07    0.36    1.44 
   user  system elapsed 
   1.25    0.28    1.53 


RUNIT TEST PROTOCOL -- Fri Oct 15 00:37:11 2021 
*********************************************** 
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 
  20.10    3.43   23.54 

iCARE.Rcheck/tests_x64/runTests.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.

> BiocGenerics:::testPackage("iCARE")

Attaching package: 'Hmisc'

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

    format.pval, units

   user  system elapsed 
   1.42    0.24    1.67 
   user  system elapsed 
   1.19    0.37    1.56 
   user  system elapsed 
   1.18    0.25    1.42 


RUNIT TEST PROTOCOL -- Fri Oct 15 00:37:38 2021 
*********************************************** 
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 
  23.03    3.34   26.37 

Example timings

iCARE.Rcheck/examples_i386/iCARE-Ex.timings

nameusersystemelapsed
bc_data000
compute.absolute.risk6.041.197.23
compute.absolute.risk.split.interval10.59 2.2812.87
model_validation0.520.090.61
plotModelValidation0.400.130.53

iCARE.Rcheck/examples_x64/iCARE-Ex.timings

nameusersystemelapsed
bc_data000
compute.absolute.risk7.250.998.23
compute.absolute.risk.split.interval11.07 1.8212.89
model_validation0.200.050.25
plotModelValidation0.190.040.24