Yuqing Zhang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/simulatorZ |
| Branch: master |
| Last Commit: bd1a092 |
| Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:30:26 -0400 (Tue, 09 Apr 2019).
| Package 1499/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| simulatorZ 1.17.0 Yuqing Zhang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
| Package: simulatorZ |
| Version: 1.17.0 |
| 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_1.17.0.tar.gz |
| StartedAt: 2019-04-09 03:48:18 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:51:52 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 214.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: simulatorZ.Rcheck |
| Warnings: 1 |
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### 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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/simulatorZ.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.17.0’
* 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 ... WARNING
Found the following significant warnings:
coxformatrices.cpp:529:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
coxformatrices.cpp:530:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
coxformatrices.cpp:570:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
coxformatrices.cpp:571:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
coxformatrices.cpp:658:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/simulatorZ.Rcheck/00install.out’ for details.
* 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
Package in Depends field not imported from: ‘BiocGenerics’
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 ... 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 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 6.912 0.075 7.06
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/simulatorZ.Rcheck/00check.log’
for details.
simulatorZ.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL simulatorZ
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘simulatorZ’ ...
** libs
clang++ -std=gnu++11 -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
^˜˜˜˜˜
coxformatrices.cpp:529:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:529:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:530:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register double temp;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:570:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register double temp;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:571:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j,k;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:571:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j,k;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:571:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j,k;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i;
^˜˜˜˜˜˜˜˜
coxformatrices.cpp:658:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register double **pointer;
^˜˜˜˜˜˜˜˜
10 warnings generated.
clang++ -std=gnu++11 -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/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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, 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, rowsum
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: affy
[1] 1
[1] "covariate: tumorstage"
RUNIT TEST PROTOCOL -- Tue Apr 9 03:51:45 2019
***********************************************
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
10.023 0.536 10.615
simulatorZ.Rcheck/simulatorZ-Ex.timings
| name | user | system | elapsed | |
| cvSubsets | 2.363 | 0.034 | 2.423 | |
| funCV | 1.747 | 0.021 | 1.781 | |
| geneFilter | 6.912 | 0.075 | 7.060 | |
| getTrueModel | 3.927 | 0.063 | 4.040 | |
| masomenos | 1.662 | 0.013 | 1.687 | |
| plusMinus | 1.652 | 0.014 | 1.677 | |
| rowCoxTests | 0.990 | 0.007 | 1.013 | |
| simBootstrap | 4.084 | 0.067 | 4.185 | |
| simData | 3.011 | 0.039 | 3.074 | |
| simTime | 3.251 | 0.031 | 3.308 | |
| zmatrix | 3.224 | 0.040 | 3.287 | |