Package: ChIPXpress

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPXpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPXpress_1.24.0.tar.gz

StartedAt: 2018-10-16 20:25:55 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:35:39 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 584.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPXpress.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPXpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPXpress_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPXpress.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPXpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPXpress’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPXpress’ can be installed ... OK
* checking installed package size ... OK
* 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
* 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: ‘ChIPXpressData’
  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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ChIPXpress 6.959  1.473  10.554
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPXpress.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPXpress
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ChIPXpress’ ...
** R
** data
** 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
* DONE (ChIPXpress)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("ChIPXpress") || stop("unable to load ChIPXpress")
Loading required package: ChIPXpress
Loading required package: ChIPXpressData
Loading required package: bigmemory
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
[1] TRUE
> BiocGenerics:::testPackage("ChIPXpress")
Downloading File 1: GSM24056...
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24056/suppl//GSM24056.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 6554536 bytes (6.3 MB)
==================================================
downloaded 6.3 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24056/suppl//GSM24056.RPT.gz?tool=geoquery'
Content type 'application/x-gzip' length 552 bytes
==================================================
downloaded 552 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24056/suppl//GSM24056.TXT.gz?tool=geoquery'
Content type 'application/x-gzip' length 2670956 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

Processing File 1: GSM24056...

Downloading File 2: GSM24058...
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24058/suppl//GSM24058.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 6590195 bytes (6.3 MB)
==================================================
downloaded 6.3 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24058/suppl//GSM24058.RPT.gz?tool=geoquery'
Content type 'application/x-gzip' length 554 bytes
==================================================
downloaded 554 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24058/suppl//GSM24058.TXT.gz?tool=geoquery'
Content type 'application/x-gzip' length 2670894 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

Processing File 2: GSM24058...
Downloading File 3: GSM24060...
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24060/suppl//GSM24060.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 6664765 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24060/suppl//GSM24060.RPT.gz?tool=geoquery'
Content type 'application/x-gzip' length 549 bytes
==================================================
downloaded 549 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM24nnn/GSM24060/suppl//GSM24060.TXT.gz?tool=geoquery'
Content type 'application/x-gzip' length 2669000 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

Processing File 3: GSM24060...
Downloading File 4: GSM94856...
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM94nnn/GSM94856/suppl//GSM94856.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 6247826 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Processing File 4: GSM94856...
Downloading File 5: GSM94857...
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM94nnn/GSM94857/suppl//GSM94857.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 6014425 bytes (5.7 MB)
==================================================
downloaded 5.7 MB

Processing File 5: GSM94857...
Downloading File 6: GSM94858...
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM94nnn/GSM94858/suppl//GSM94858.CEL.gz?tool=geoquery'
Content type 'application/x-gzip' length 6029560 bytes (5.8 MB)
==================================================
downloaded 5.8 MB

Processing File 6: GSM94858...
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: org.Mm.eg.db


Success!
4773 out of 5158 (92.5%) genes processed


RUNIT TEST PROTOCOL -- Tue Oct 16 20:35:27 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPXpress RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'mouse4302cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'mouse4302cdf' 
> 
> proc.time()
   user  system elapsed 
289.989  73.096 372.453 

name	user	system	elapsed
ChIPXpress	6.959	1.473	10.554
Oct4ESC_ChIPgenes	0.047	0.004	0.051
buildDatabase	0.006	0.001	0.008
cleanDatabase	0.004	0.001	0.005