Package: ppiData

Version: 0.24.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ppiData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ppiData_0.24.0.tar.gz

StartedAt: 2020-04-14 12:54:41 -0400 (Tue, 14 Apr 2020)

EndedAt: 2020-04-14 12:56:00 -0400 (Tue, 14 Apr 2020)

EllapsedTime: 78.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ppiData.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ppiData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ppiData_0.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/ppiData.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiData/DESCRIPTION’ ... OK
* this is package ‘ppiData’ version ‘0.24.0’
* 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 ‘ppiData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘graph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
collectIntactPPIData: no visible binding for global variable ‘recover’
collectIntactPPIData: no visible global function definition for ‘data’
collectIntactPPIData: no visible binding for global variable
  ‘tableList’
collectIntactPPIData: no visible binding for global variable ‘sWAC2Sys’
collectIntactPPIData : <anonymous>: no visible binding for global
  variable ‘tableList’
collectIntactPPIData : <anonymous> : <anonymous>: no visible binding
  for global variable ‘tableList’
intAct2Sys: no visible binding for global variable ‘recover’
map2Systematic: no visible binding for global variable
  ‘org.Sc.sgdCOMMON2ORF’
map2Systematic: no visible binding for global variable
  ‘org.Sc.sgdALIAS’
map2Systematic: no visible binding for global variable
  ‘org.Sc.sgdREJECTORF’
Undefined global functions or variables:
  data org.Sc.sgdALIAS org.Sc.sgdCOMMON2ORF org.Sc.sgdREJECTORF recover
  sWAC2Sys tableList
Consider adding
  importFrom("utils", "data", "recover")
to your NAMESPACE file.
* 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 ... WARNING
  Warning: large data file saved inefficiently:
               size ASCII compress
  ppipred.rda 896Kb FALSE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  Gavin2002BPGraph.rda       17Kb     10Kb       xz
  Gavin2006BPGraph.rda       50Kb     27Kb    bzip2
  Hazbun2003BPGraph.rda      20Kb      8Kb       xz
  Ho2002BPGraph.rda          19Kb      9Kb       xz
  Ito2001BPGraph.rda         33Kb     15Kb       xz
  ItoFull2001BPGraph.rda     33Kb     15Kb       xz
  Krogan2006BPGraph.rda     151Kb     84Kb    bzip2
  intActPPIData.rda         114Kb     63Kb       xz
  ppipred.rda               896Kb     85Kb       xz
  sWAC2Sys.rda               35Kb     18Kb       xz
  stochasticBaits.rda        31Kb     20Kb    bzip2
  tableList.rda             2.0Mb    783Kb       xz
  twTableAPMS.rda            24Kb     15Kb    bzip2
  viableBaits.rda            22Kb     14Kb       xz
  viablePrey.rda             47Kb     30Kb    bzip2
  y2h.rda                    76Kb     47Kb    bzip2
  y2hSysGW.rda               71Kb     44Kb    bzip2
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
collectIntactPPIData 6.244  0.028   6.276
* 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-data-experiment/meat/ppiData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ppiData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘ppiData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ppiData)

name	user	system	elapsed
Cagney2001BPGraph	0.008	0.004	0.013
Gavin2002BPGraph	0.000	0.000	0.001
Gavin2006bPGraph	0.004	0.000	0.001
Hazbun2003BPGraph	0.000	0.000	0.001
Ho2002BPGraph	0.000	0.000	0.001
Ito2001BPGraph	0.004	0.000	0.000
ItoCore2001BPGraph	0.000	0.000	0.001
ItoFull2001BPGraph	0.000	0.000	0.001
Krogan2004BPGraph	0.004	0.000	0.001
Krogan2006BPGraph	0.000	0.000	0.001
Tong2002BPGraph	0.000	0.000	0.001
Uetz2000BPGraph1	0.004	0.000	0.001
Uetz2000BPGraph2	0	0	0
Zhao2005BPGraph	0.000	0.000	0.001
bpExperimentNames	0.004	0.000	0.003
collectIntactPPIData	6.244	0.028	6.276
createBPList	0.204	0.000	0.204
intActPPIData	0.000	0.000	0.001
map2Systematic	0.000	0.000	0.002
ppipred	0.000	0.000	0.001
sWAC2Sys	0.000	0.000	0.001
stochasticBaits	0.004	0.000	0.003
tableList	0	0	0
twTableAPMS	0.004	0.000	0.001
twTableY2H	0.000	0.000	0.001
viableProteins	0.004	0.000	0.006
y2h	0	0	0
y2hSysGW	0.000	0.004	0.006