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BioC 3.4: CHECK report for psygenet2r on moscato1

This page was generated on 2016-09-21 03:48:08 -0700 (Wed, 21 Sep 2016).

Package 939/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psygenet2r 1.5.0
Alba Gutierrez-Sacristan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/psygenet2r
Last Changed Rev: 120782 / Revision: 121152
Last Changed Date: 2016-09-07 01:25:21 -0700 (Wed, 07 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: psygenet2r
Version: 1.5.0
Command: rm -rf psygenet2r.buildbin-libdir psygenet2r.Rcheck && mkdir psygenet2r.buildbin-libdir psygenet2r.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psygenet2r.buildbin-libdir psygenet2r_1.5.0.tar.gz >psygenet2r.Rcheck\00install.out 2>&1 && cp psygenet2r.Rcheck\00install.out psygenet2r-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=psygenet2r.buildbin-libdir --install="check:psygenet2r-install.out" --force-multiarch --no-vignettes --timings psygenet2r_1.5.0.tar.gz
StartedAt: 2016-09-20 14:22:31 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 14:28:51 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 380.6 seconds
RetCode: 0
Status:  OK  
CheckDir: psygenet2r.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf psygenet2r.buildbin-libdir psygenet2r.Rcheck && mkdir psygenet2r.buildbin-libdir psygenet2r.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psygenet2r.buildbin-libdir psygenet2r_1.5.0.tar.gz >psygenet2r.Rcheck\00install.out 2>&1 && cp psygenet2r.Rcheck\00install.out psygenet2r-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=psygenet2r.buildbin-libdir --install="check:psygenet2r-install.out" --force-multiarch --no-vignettes --timings psygenet2r_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/psygenet2r.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 'psygenet2r/DESCRIPTION' ... OK
* this is package 'psygenet2r' version '1.5.0'
* 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 'psygenet2r' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
 NOTE
Authors@R field gives no person with maintainer role, valid email
address and non-empty name.
* 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 ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.category_plot: possible error in psygenetGene(x, databse = "ALL"):
  unused argument (databse = "ALL")
.category_plot: no visible binding for global variable 'category'
.category_plot: no visible binding for global variable 'value'
.category_plot: no visible binding for global variable 'variable'
.gene_plot: possible error in psygenetGene(x, databse = "ALL"): unused
  argument (databse = "ALL")
.gene_plot: no visible binding for global variable 'gene'
.gene_plot: no visible binding for global variable 'value'
.gene_plot: no visible binding for global variable 'variable'
.index_plot: possible error in psygenetGene(x, databse = "ALL"): unused
  argument (databse = "ALL")
.index_plot: no visible binding for global variable 'Category'
.index_plot: no visible binding for global variable 'value'
.index_plot: no visible binding for global variable 'variable'
.pie_plot: possible error in psygenetGene(x, databse = "ALL", verbose =
  verbose): unused argument (databse = "ALL")
.pie_plot: no visible global function definition for 'pie'
ListPsyGeNETIds: no visible global function definition for 'read.csv'
disGenetCurated: no visible global function definition for 'read.csv'
disgenetAll: no visible global function definition for 'read.csv'
enrichedPD : <anonymous>: no visible global function definition for
  'phyper'
getUMLs: no visible global function definition for 'read.csv'
multipleInput: no visible global function definition for 'new'
pantherGraphic: no visible binding for global variable 'Var1'
pantherGraphic: no visible binding for global variable 'perc'
pantherGraphic: no visible binding for global variable 'diseases'
plot_pmids_barplot: no visible binding for global variable
  'c2.Disease_code'
plot_pmids_barplot: no visible binding for global variable
  'c0.Number_of_Abstracts'
plot_pmids_barplot: no visible binding for global variable
  'c1.Gene_Symbol'
plot_psy_heatmap: no visible binding for global variable
  'c2.PsychiatricDisorder'
plot_psy_heatmap: no visible binding for global variable
  'c1.Gene_Symbol'
plot_psy_heatmap: no visible binding for global variable 'value'
plot_psy_heatmapDisease: no visible binding for global variable
  'c2.DiseaseName'
plot_psy_heatmapDisease: no visible binding for global variable
  'c1.Gene_Symbol'
plot_psy_heatmapDisease: no visible binding for global variable
  'c0.Score'
plot_psy_heatmapGenes: no visible binding for global variable
  'c1.Gene_Symbol'
plot_psy_heatmapGenes: no visible binding for global variable
  'c2.DiseaseName'
plot_psy_heatmapGenes: no visible binding for global variable
  'c0.Score'
psyGenDisId: no visible global function definition for 'read.csv'
psyPanther: no visible global function definition for 'read.csv'
psygenetAll: no visible global function definition for 'read.csv'
psygenetDisease: no visible global function definition for 'read.csv'
psygenetDisease: no visible global function definition for 'new'
psygenetDiseaseSentences: no visible global function definition for
  'read.csv'
psygenetDiseaseSentences: no visible global function definition for
  'new'
psygenetGene: no visible global function definition for 'read.csv'
psygenetGene: no visible global function definition for 'new'
psygenetGeneSentences: no visible global function definition for
  'read.csv'
psygenetGeneSentences: no visible global function definition for 'new'
singleInput: no visible global function definition for 'combn'
singleInput: no visible global function definition for 'new'
singleInput.genes: no visible global function definition for 'new'
topAnatEnrichment: no visible binding for global variable 'database'
topAnatEnrichment: no visible global function definition for
  'read.delim'
topAnatEnrichment: no visible binding for global variable
  'genesOfInterest'
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  'Disease1'
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  'Disease2'
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  'JaccardIndex'
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  'value'
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  'variable'
Undefined global functions or variables:
  Category Disease1 Disease2 JaccardIndex Var1 c0.Number_of_Abstracts
  c0.Score c1.Gene_Symbol c2.DiseaseName c2.Disease_code
  c2.PsychiatricDisorder category combn database diseases gene
  genesOfInterest new perc phyper pie read.csv read.delim value
  variable
Consider adding
  importFrom("graphics", "pie")
  importFrom("methods", "new")
  importFrom("stats", "phyper")
  importFrom("utils", "combn", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
pantherGraphic-methods    0.60   0.00    7.41
psygenetGeneSentences     0.42   0.01   23.53
JaccardIndexPsy-class     0.25   0.00    6.34
jaccardEstimation-methods 0.12   0.00    5.60
enrichedPD-methods        0.11   0.00    5.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
pantherGraphic-methods    0.59   0.02    7.52
psygenetGeneSentences     0.58   0.02   23.55
JaccardIndexPsy-class     0.30   0.03    5.48
enrichedPD-methods        0.09   0.00    6.09
jaccardEstimation-methods 0.08   0.00    5.23
psygenetGene-methods      0.04   0.00    7.74
* 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 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/psygenet2r.Rcheck/00check.log'
for details.


psygenet2r.Rcheck/00install.out:


install for i386

* installing *source* package 'psygenet2r' ...
It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'psygenet2r'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'psygenet2r' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psygenet2r' as psygenet2r_1.5.0.zip
* DONE (psygenet2r)

psygenet2r.Rcheck/examples_i386/psygenet2r-Ex.timings:

nameusersystemelapsed
JaccardIndexPsy-class0.250.006.34
enrichedPD-methods0.110.005.61
extract000
extractSentences0.020.000.02
getUMLs-methods0.000.000.86
jaccardEstimation-methods0.120.005.60
ndisease000
ngene000
pantherGraphic-methods0.600.007.41
plot-DataGeNET.Psy-ANY-method0.100.000.09
plot-JaccardIndexPsy-ANY-method000
psygenetDisease-methods0.030.004.43
psygenetDiseaseSentences0.050.002.42
psygenetGene-methods0.080.003.21
psygenetGeneSentences 0.42 0.0123.53
qr000
topAnatEnrichment-methods000

psygenet2r.Rcheck/examples_x64/psygenet2r-Ex.timings:

nameusersystemelapsed
JaccardIndexPsy-class0.300.035.48
enrichedPD-methods0.090.006.09
extract0.020.000.02
extractSentences000
getUMLs-methods0.010.000.84
jaccardEstimation-methods0.080.005.23
ndisease0.020.000.01
ngene000
pantherGraphic-methods0.590.027.52
plot-DataGeNET.Psy-ANY-method0.120.010.14
plot-JaccardIndexPsy-ANY-method000
psygenetDisease-methods0.050.004.18
psygenetDiseaseSentences0.020.003.25
psygenetGene-methods0.040.007.74
psygenetGeneSentences 0.58 0.0223.55
qr000
topAnatEnrichment-methods000