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 ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings psygenet2r_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/psygenet2r.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pantherGraphic-methods 0.476 0.012 6.954
psygenetGeneSentences 0.444 0.008 23.513
JaccardIndexPsy-class 0.252 0.008 5.452
jaccardEstimation-methods 0.092 0.008 5.324
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/home/biocbuild/bbs-3.4-bioc/meat/psygenet2r.Rcheck/00check.log’
for details.
* 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
* DONE (psygenet2r)