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BioC 3.4: CHECK report for iCARE on zin1

This page was generated on 2016-09-21 03:40:31 -0700 (Wed, 21 Sep 2016).

Package 595/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCARE 1.1.0
Bill Wheeler
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iCARE
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iCARE
Version: 1.1.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iCARE_1.1.0.tar.gz
StartedAt: 2016-09-20 07:58:50 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:59:10 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 20.5 seconds
RetCode: 0
Status:  OK 
CheckDir: iCARE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iCARE_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/iCARE.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.0’
* 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 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 loading without being on the library search path ... 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
PRS_research: no visible global function definition for ‘rnorm’
PRS_research: no visible global function definition for ‘weighted.mean’
check_competing_rates: no visible global function definition for
  ‘read.table’
check_disease_rates: no visible global function definition for
  ‘read.table’
computeAbsoluteRisk: no visible global function definition for
  ‘weighted.mean’
get_beta_given_names: no visible global function definition for
  ‘model.matrix’
get_cutpoints: no visible global function definition for ‘sd’
get_cutpoints: no visible global function definition for ‘quantile’
handle_missing_data: no visible global function definition for
  ‘weighted.mean’
make_design_matrix_covs: no visible global function definition for
  ‘model.matrix’
make_design_matrix_dist: no visible global function definition for
  ‘model.matrix’
process_triple_check: no visible global function definition for
  ‘relevel’
sim_snps: no visible global function definition for ‘runif’
Undefined global functions or variables:
  model.matrix quantile read.table relevel rnorm runif sd weighted.mean
Consider adding
  importFrom("stats", "model.matrix", "quantile", "relevel", "rnorm",
             "runif", "sd", "weighted.mean")
  importFrom("utils", "read.table")
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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/iCARE.Rcheck/00check.log’
for details.


iCARE.Rcheck/00install.out:

* installing *source* package ‘iCARE’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c source.c -o source.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o iCARE.so source.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/iCARE.Rcheck/iCARE/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iCARE)

iCARE.Rcheck/iCARE-Ex.timings:

nameusersystemelapsed
bc_data0.0120.0000.014
compute.absolute.risk0.7000.0160.717
compute.absolute.risk.split.interval1.8800.1562.036