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BioC 3.4: CHECK report for BPRMeth on morelia

This page was generated on 2017-04-15 16:28:15 -0400 (Sat, 15 Apr 2017).

Package 138/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BPRMeth 1.0.0
Chantriolnt-Andreas Kapourani
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/BPRMeth
Last Changed Rev: 123171 / Revision: 128728
Last Changed Date: 2016-10-28 18:04:29 -0400 (Fri, 28 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: BPRMeth
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BPRMeth_1.0.0.tar.gz
StartedAt: 2017-04-14 23:20:41 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:24:20 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 219.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BPRMeth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BPRMeth_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BPRMeth.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BPRMeth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BPRMeth’ version ‘1.0.0’
* 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 ‘BPRMeth’ 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
boxplot_cluster_gex 37.820  0.194  38.034
bpr_cluster_wrap    34.952  0.145  35.138
plot_cluster_prof   34.831  0.133  34.975
bpr_optimize         5.444  0.020   5.474
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/BPRMeth.Rcheck/00check.log’
for details.


BPRMeth.Rcheck/00install.out:

* installing *source* package ‘BPRMeth’ ...
** 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
* DONE (BPRMeth)

BPRMeth.Rcheck/BPRMeth-Ex.timings:

nameusersystemelapsed
boxplot_cluster_gex37.820 0.19438.034
bpr_cluster_wrap34.952 0.14535.138
bpr_optimize5.4440.0205.474
bpr_predict_wrap2.7690.0072.777
create_basis0.0020.0000.002
create_methyl_region0.7400.0120.751
create_prom_region0.2590.0040.263
eval_functions0.0040.0000.005
plot_cluster_prof34.831 0.13334.975
plot_fitted_profiles3.3730.0083.382
plot_scatter_gex3.0350.0123.046
pool_bs_seq_rep0.7350.0220.757
predict_model_gex0.0060.0000.006
preprocess_bs_seq0.6180.0100.629
preprocess_final_HTS_data0.6730.0070.679
process_haib_caltech_wrap0.8700.0150.884
read_bs_bismark_cov0.0010.0000.001
read_bs_encode_haib0.3640.0050.369
read_chrom_size0.0050.0010.005
read_encode_cgi0.0000.0000.001
read_rna_encode_caltech0.2270.0030.229
train_model_gex0.0130.0000.014