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BioC 3.4: CHECK report for metagenomeFeatures on moscato1

This page was generated on 2016-09-21 03:47:40 -0700 (Wed, 21 Sep 2016).

Package 723/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeFeatures 1.3.2
Nathan D. Olson
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeFeatures
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: metagenomeFeatures
Version: 1.3.2
Command: rm -rf metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && mkdir metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_1.3.2.tar.gz >metagenomeFeatures.Rcheck\00install.out 2>&1 && cp metagenomeFeatures.Rcheck\00install.out metagenomeFeatures-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=metagenomeFeatures.buildbin-libdir --install="check:metagenomeFeatures-install.out" --force-multiarch --no-vignettes --timings metagenomeFeatures_1.3.2.tar.gz
StartedAt: 2016-09-20 11:48:45 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:53:42 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 296.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: metagenomeFeatures.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && mkdir metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_1.3.2.tar.gz >metagenomeFeatures.Rcheck\00install.out 2>&1 && cp metagenomeFeatures.Rcheck\00install.out metagenomeFeatures-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=metagenomeFeatures.buildbin-libdir --install="check:metagenomeFeatures-install.out" --force-multiarch --no-vignettes --timings metagenomeFeatures_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/metagenomeFeatures.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagenomeFeatures/DESCRIPTION' ... OK
* this is package 'metagenomeFeatures' version '1.3.2'
* 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 'metagenomeFeatures' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.7Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  34.3Mb
* 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
.select.taxa: no visible binding for global variable 'Keys'
.select.taxa: no visible binding for global variable '.'
aggregate_taxa: no visible binding for global variable '.'
aggregate_taxa: no visible binding for global variable 'index'
aggregate_taxa: no visible global function definition for
  'newMRexperiment'
Undefined global functions or variables:
  . Keys index newMRexperiment
* checking Rd files ... WARNING
checkRd: (5) aggregate_taxa.Rd:0-40: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'msd16s_query_df.Rd':
  'metagenomeAnnotation-class' 'annotate'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'msd16s_metagenomeAnnotation'
Undocumented data sets:
  'msd16s_metagenomeAnnotation'
Undocumented S4 methods:
  generic 'taxa_columns' and siglist 'MgDb'
  generic 'taxa_keys' and siglist 'MgDb'
  generic 'taxa_keytypes' and siglist 'MgDb'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
** running examples for arch 'x64' ... OK
* 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: 3 WARNINGs, 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/metagenomeFeatures.Rcheck/00check.log'
for details.


metagenomeFeatures.Rcheck/00install.out:


install for i386

* installing *source* package 'metagenomeFeatures' ...
** 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 'metagenomeFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagenomeFeatures' as metagenomeFeatures_1.3.2.zip
* DONE (metagenomeFeatures)

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

nameusersystemelapsed
MgDb-class0.640.020.66
aggregate_taxa000
get_demoMgDb0.580.010.59
mgF_meta000
mgF_seq000
mgF_taxa000
mgF_tree000
mgFeatures-class0.000.000.02
mgQuery000
mgdb_meta000
mgdb_seq000
mgdb_taxa000
mgdb_tree000
msd16s_query_df0.020.000.01
select-MgDb-method0.730.000.74
taxa_columns0.330.000.32
taxa_keys0.340.000.35
taxa_keytypes0.340.000.34
taxa_levels000

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

nameusersystemelapsed
MgDb-class0.350.010.40
aggregate_taxa000
get_demoMgDb0.320.000.33
mgF_meta000
mgF_seq000
mgF_taxa000
mgF_tree000
mgFeatures-class000
mgQuery0.020.000.02
mgdb_meta000
mgdb_seq000
mgdb_taxa000
mgdb_tree000
msd16s_query_df000
select-MgDb-method1.320.051.59
taxa_columns0.310.000.31
taxa_keys0.300.030.33
taxa_keytypes0.650.000.66
taxa_levels000