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BioC 3.4: CHECK report for metagenomeFeatures on tokay1

This page was generated on 2017-04-15 16:20:24 -0400 (Sat, 15 Apr 2017).

Package 745/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeFeatures 1.4.0
Nathan D. Olson
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/metagenomeFeatures
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: 1.4.0
Command: rm -rf metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && mkdir metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_1.4.0.tar.gz >metagenomeFeatures.Rcheck\00install.out 2>&1 && cp metagenomeFeatures.Rcheck\00install.out metagenomeFeatures-install.out && C:\Users\biocbuild\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_1.4.0.tar.gz
StartedAt: 2017-04-14 23:25:34 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:29:59 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 265.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: metagenomeFeatures.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && mkdir metagenomeFeatures.buildbin-libdir metagenomeFeatures.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_1.4.0.tar.gz >metagenomeFeatures.Rcheck\00install.out 2>&1 && cp metagenomeFeatures.Rcheck\00install.out metagenomeFeatures-install.out  && C:\Users\biocbuild\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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/metagenomeFeatures.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.4.0'
* 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 whether package 'metagenomeFeatures' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
* 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
.mgDb_annotateFeatures: no visible binding for global variable
  'db_keys'
.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'
vignette_pheno_data: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  . Keys db_keys index newMRexperiment read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
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 ... WARNING
Undocumented arguments in documentation object 'annotateFeatures'
  'query_key'
Documented arguments not in \usage in documentation object 'annotateFeatures':
  'db_keys' 'query_df'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/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_1.4.0.zip
* DONE (metagenomeFeatures)

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

nameusersystemelapsed
MgDb-class0.110.000.11
aggregate_taxa000
annotateFeatures-MgDb-method0.220.030.25
annotateMRexp_fData-MgDb-method000
get_demoMgDb0.440.000.44
get_mockMgDb0.110.000.11
mgF_meta0.010.020.03
mgF_seq0.360.000.36
mgF_taxa0.050.000.04
mgF_tree0.030.020.05
mgFeatures-class0.020.000.02
mgQuery000
mgdb_meta0.090.060.15
mgdb_seq0.190.000.19
mgdb_taxa0.130.040.17
mgdb_tree0.140.000.14
mock_mgF000
mock_query_df000
select-MgDb-method0.240.050.28
taxa_columns0.150.000.16
taxa_keys0.180.000.17
taxa_keytypes0.170.000.17
taxa_levels000

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

nameusersystemelapsed
MgDb-class0.120.000.18
aggregate_taxa000
annotateFeatures-MgDb-method0.220.030.25
annotateMRexp_fData-MgDb-method000
get_demoMgDb0.100.000.09
get_mockMgDb0.090.000.10
mgF_meta0.050.000.04
mgF_seq0.040.000.05
mgF_taxa0.490.000.49
mgF_tree0.410.000.40
mgFeatures-class000
mgQuery000
mgdb_meta0.100.000.11
mgdb_seq0.130.000.13
mgdb_taxa0.110.000.11
mgdb_tree0.080.010.09
mock_mgF0.000.020.02
mock_query_df000
select-MgDb-method0.580.030.60
taxa_columns0.070.010.10
taxa_keys0.100.020.11
taxa_keytypes0.080.010.09
taxa_levels000