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CHECK report for iCARE on malbec2

This page was generated on 2019-04-09 11:44:35 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:iCARE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iCARE_1.11.6.tar.gz
StartedAt: 2019-04-09 01:17:57 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:20:02 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 124.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: iCARE.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:iCARE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iCARE_1.11.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/iCARE.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
compute.absolute.risk.split.interval 10.973  1.151  12.164
compute.absolute.risk                 7.713  0.934   8.683
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/iCARE.Rcheck/00check.log’
for details.



Installation output

iCARE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL iCARE
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘iCARE’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c source.c -o source.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o iCARE.so source.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-iCARE/00new/iCARE/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iCARE)

Tests output

iCARE.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.761   0.255   2.043 
   user  system elapsed 
  1.911   0.036   1.970 
   user  system elapsed 
  1.518   0.037   1.554 


RUNIT TEST PROTOCOL -- Tue Apr  9 01:19:59 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 
 20.912   1.534  22.557 

Example timings

iCARE.Rcheck/iCARE-Ex.timings

nameusersystemelapsed
bc_data0.0030.0000.003
compute.absolute.risk7.7130.9348.683
compute.absolute.risk.split.interval10.973 1.15112.164
model_validation0.2910.0120.304
plotModelValidation0.4510.0480.501