Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for simulatorZ on merida2

This page was generated on 2019-04-09 13:30:26 -0400 (Tue, 09 Apr 2019).

Package 1499/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simulatorZ 1.17.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  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: 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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

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/3.6/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)

Tests output

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 

Example timings

simulatorZ.Rcheck/simulatorZ-Ex.timings

nameusersystemelapsed
cvSubsets2.3630.0342.423
funCV1.7470.0211.781
geneFilter6.9120.0757.060
getTrueModel3.9270.0634.040
masomenos1.6620.0131.687
plusMinus1.6520.0141.677
rowCoxTests0.9900.0071.013
simBootstrap4.0840.0674.185
simData3.0110.0393.074
simTime3.2510.0313.308
zmatrix3.2240.0403.287