Bill Wheeler
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/iCARE |
| Branch: RELEASE_3_6 |
| Last Commit: 6808cb8 |
| Last Changed Date: 2017-10-30 12:41:12 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:23 -0400 (Thu, 12 Apr 2018).
| Package 673/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iCARE 1.6.0 Bill Wheeler
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: iCARE |
| Version: 1.6.0 |
| Command: rm -rf iCARE.buildbin-libdir iCARE.Rcheck && mkdir iCARE.buildbin-libdir iCARE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iCARE.buildbin-libdir iCARE_1.6.0.tar.gz >iCARE.Rcheck\00install.out 2>&1 && cp iCARE.Rcheck\00install.out iCARE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iCARE.buildbin-libdir --install="check:iCARE-install.out" --force-multiarch --no-vignettes --timings iCARE_1.6.0.tar.gz |
| StartedAt: 2018-04-12 00:46:57 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:47:44 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 46.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iCARE.Rcheck |
| Warnings: 0 |
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### Running command:
###
### rm -rf iCARE.buildbin-libdir iCARE.Rcheck && mkdir iCARE.buildbin-libdir iCARE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iCARE.buildbin-libdir iCARE_1.6.0.tar.gz >iCARE.Rcheck\00install.out 2>&1 && cp iCARE.Rcheck\00install.out iCARE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iCARE.buildbin-libdir --install="check:iCARE-install.out" --force-multiarch --no-vignettes --timings iCARE_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/iCARE.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.6.0'
* 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
** checking loading without being on the library search path ... 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 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 ... 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-3.6-bioc/meat/iCARE.buildbin-libdir/iCARE/libs/i386/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/iCARE.Rcheck/00check.log'
for details.
iCARE.Rcheck/00install.out
install for i386
* installing *source* package 'iCARE' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c source.c -o source.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o iCARE.dll tmp.def source.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/iCARE.buildbin-libdir/iCARE/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'iCARE' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c source.c -o source.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o iCARE.dll tmp.def source.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/iCARE.buildbin-libdir/iCARE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCARE' as iCARE_1.6.0.zip
* DONE (iCARE)
In R CMD INSTALL
In R CMD INSTALL
|
iCARE.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
user system elapsed
0.17 0.01 0.19
user system elapsed
0.19 0.00 0.19
user system elapsed
0.18 0.06 0.24
RUNIT TEST PROTOCOL -- Thu Apr 12 00:47:34 2018
***********************************************
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
5.00 0.50 5.46
|
iCARE.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
user system elapsed
0.20 0.00 0.21
user system elapsed
0.13 0.00 0.12
user system elapsed
0.18 0.02 0.20
RUNIT TEST PROTOCOL -- Thu Apr 12 00:47:40 2018
***********************************************
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
5.35 0.32 5.68
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iCARE.Rcheck/examples_i386/iCARE-Ex.timings
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iCARE.Rcheck/examples_x64/iCARE-Ex.timings
|