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BioC 3.6: CHECK report for DaMiRseq on tokay1

This page was generated on 2017-08-16 13:37:41 -0400 (Wed, 16 Aug 2017).

Package 317/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DaMiRseq 1.1.0
Mattia Chiesa
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DaMiRseq
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DaMiRseq
Version: 1.1.0
Command: rm -rf DaMiRseq.buildbin-libdir DaMiRseq.Rcheck && mkdir DaMiRseq.buildbin-libdir DaMiRseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DaMiRseq.buildbin-libdir DaMiRseq_1.1.0.tar.gz >DaMiRseq.Rcheck\00install.out 2>&1 && cp DaMiRseq.Rcheck\00install.out DaMiRseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DaMiRseq.buildbin-libdir --install="check:DaMiRseq-install.out" --force-multiarch --no-vignettes --timings DaMiRseq_1.1.0.tar.gz
StartedAt: 2017-08-15 22:49:36 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:59:53 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 616.7 seconds
RetCode: 0
Status:  OK  
CheckDir: DaMiRseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DaMiRseq.buildbin-libdir DaMiRseq.Rcheck && mkdir DaMiRseq.buildbin-libdir DaMiRseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DaMiRseq.buildbin-libdir DaMiRseq_1.1.0.tar.gz >DaMiRseq.Rcheck\00install.out 2>&1 && cp DaMiRseq.Rcheck\00install.out DaMiRseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DaMiRseq.buildbin-libdir --install="check:DaMiRseq-install.out" --force-multiarch --no-vignettes --timings DaMiRseq_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DaMiRseq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DaMiRseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DaMiRseq' version '1.1.0'
* package encoding: UTF-8
* 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 'DaMiRseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
* 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
DaMiR.Allplot: warning in pheatmap(sampleDistMatrix,
  clustering_distance_rows = mydist, clustering_distance_cols = mydist,
  col = colors, breaks = seque, annotation_col = df): partial argument
  match of 'col' to 'color'
DaMiR.Clustplot: warning in pheatmap(count_data,
  clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale
  = "row", col = colors, annotation_col = df): partial argument match
  of 'col' to 'color'
DaMiR.Allplot: no visible binding for global variable 'X1'
DaMiR.Allplot: no visible binding for global variable 'X2'
DaMiR.EnsembleLearning: no visible binding for global variable
  'Predictors'
DaMiR.EnsembleLearning: no visible binding for global variable
  'Accuracy'
DaMiR.MDSplot: no visible binding for global variable 'X1'
DaMiR.MDSplot: no visible binding for global variable 'X2'
Undefined global functions or variables:
  Accuracy Predictors X1 X2
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DaMiR.FSort            15.35   0.01   15.36
DaMiR.EnsembleLearning 10.13   0.00   10.13
DaMiR.FSelect           4.95   0.11    5.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DaMiR.FSort            19.61   0.02   19.63
DaMiR.EnsembleLearning 11.30   0.00   11.30
DaMiR.FSelect           5.31   0.34    5.66
DaMiR.Allplot           5.00   0.06    5.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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/DaMiRseq.Rcheck/00check.log'
for details.


DaMiRseq.Rcheck/00install.out:


install for i386

* installing *source* package 'DaMiRseq' ...
** 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

install for x64

* installing *source* package 'DaMiRseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DaMiRseq' as DaMiRseq_1.1.0.zip
* DONE (DaMiRseq)

DaMiRseq.Rcheck/examples_i386/DaMiRseq-Ex.timings:

nameusersystemelapsed
DaMiR.Allplot4.330.224.54
DaMiR.Clustplot0.840.030.88
DaMiR.EnsembleLearning10.13 0.0010.13
DaMiR.FBest0.030.010.05
DaMiR.FReduct0.010.020.03
DaMiR.FSelect4.950.115.07
DaMiR.FSort15.35 0.0115.36
DaMiR.MDSplot0.190.000.19
DaMiR.SV0.690.030.72
DaMiR.SVadjust0.110.040.14
DaMiR.corrplot0.040.010.06
DaMiR.goldenDice000

DaMiRseq.Rcheck/examples_x64/DaMiRseq-Ex.timings:

nameusersystemelapsed
DaMiR.Allplot5.000.065.06
DaMiR.Clustplot0.890.010.90
DaMiR.EnsembleLearning11.3 0.011.3
DaMiR.FBest0.040.000.04
DaMiR.FReduct0.020.020.03
DaMiR.FSelect5.310.345.66
DaMiR.FSort19.61 0.0219.63
DaMiR.MDSplot0.250.020.26
DaMiR.SV1.360.071.44
DaMiR.SVadjust0.140.020.16
DaMiR.corrplot0.050.000.04
DaMiR.goldenDice000