Yuqing Zhang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/simulatorZ |
| Branch: RELEASE_3_7 |
| Last Commit: 4fe7390 |
| Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:53:36 -0400 (Wed, 17 Oct 2018).
| Package 1379/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| simulatorZ 1.14.0 Yuqing Zhang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: simulatorZ |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:simulatorZ.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings simulatorZ_1.14.0.tar.gz |
| StartedAt: 2018-10-17 00:07:12 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:11:17 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 245.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: simulatorZ.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:simulatorZ.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings simulatorZ_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/simulatorZ.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simulatorZ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simulatorZ’ version ‘1.14.0’
* 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 ‘simulatorZ’ 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 ... NOTE
Namespaces in Imports field not imported from:
‘IRanges’ ‘S4Vectors’
All declared Imports should be used.
Packages in Depends field not imported from:
‘BiocGenerics’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fastCox: no visible global function definition for ‘pnorm’
fastCox: no visible global function definition for ‘new’
geneFilter: no visible global function definition for ‘cor’
getMatrix: no visible global function definition for ‘is’
masomenos: no visible global function definition for ‘is’
plusMinus: no visible binding for global variable ‘sd’
plusMinus: no visible binding for global variable ‘quantile’
plusMinus: no visible global function definition for ‘new’
rowCoxTests: no visible global function definition for ‘pnorm’
simData: no visible global function definition for ‘is’
simTime: no visible global function definition for ‘runif’
Undefined global functions or variables:
cor is new pnorm quantile runif sd
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "cor", "pnorm", "quantile", "runif", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneFilter 13.762 0.425 14.327
zmatrix 7.188 0.131 7.397
getTrueModel 7.066 0.088 7.202
simTime 6.764 0.082 6.906
simBootstrap 6.420 0.108 6.566
simData 5.572 0.052 5.650
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/simulatorZ.Rcheck/00check.log’
for details.
simulatorZ.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL simulatorZ
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘simulatorZ’ ...
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:79:17: warning: suggest braces around initialization of subobject [-Wmissing-braces]
NULL
^˜˜˜
{ }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:100:18: note: expanded from macro 'NULL'
# define NULL __null
^˜˜˜˜˜
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o simulatorZ.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/simulatorZ/libs
** R
** 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
* DONE (simulatorZ)
simulatorZ.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("simulatorZ")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: affy
[1] 1
[1] "covariate: tumorstage"
RUNIT TEST PROTOCOL -- Wed Oct 17 00:11:12 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
simulatorZ RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
10.033 0.524 11.253
simulatorZ.Rcheck/simulatorZ-Ex.timings
| name | user | system | elapsed | |
| cvSubsets | 2.309 | 0.052 | 3.010 | |
| funCV | 1.706 | 0.024 | 1.737 | |
| geneFilter | 13.762 | 0.425 | 14.327 | |
| getTrueModel | 7.066 | 0.088 | 7.202 | |
| masomenos | 1.564 | 0.014 | 1.587 | |
| plusMinus | 1.439 | 0.014 | 1.460 | |
| rowCoxTests | 0.948 | 0.029 | 0.988 | |
| simBootstrap | 6.420 | 0.108 | 6.566 | |
| simData | 5.572 | 0.052 | 5.650 | |
| simTime | 6.764 | 0.082 | 6.906 | |
| zmatrix | 7.188 | 0.131 | 7.397 | |