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BioC 3.5: CHECK report for SpidermiR on veracruz2

This page was generated on 2017-08-16 13:34:24 -0400 (Wed, 16 Aug 2017).

Package 1253/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpidermiR 1.6.3
Claudia Cava
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/SpidermiR
Last Changed Rev: 130683 / Revision: 131943
Last Changed Date: 2017-06-26 11:55:09 -0400 (Mon, 26 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SpidermiR
Version: 1.6.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.6.3.tar.gz
StartedAt: 2017-08-16 08:29:49 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 08:35:53 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 364.1 seconds
RetCode: 0
Status:  OK 
CheckDir: SpidermiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.6.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SpidermiR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpidermiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpidermiR’ version ‘1.6.3’
* 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 ‘SpidermiR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.SpidermiRvisualize_gene: possible error in simpleNetwork(NetworkData,
  linkColour = "gray", textColour = "black", zoom = TRUE): unused
  argument (textColour = "black")
SpidermiRvisualize_plot_target: no visible binding for global variable
  ‘miRNAs’
SpidermiRvisualize_plot_target: no visible binding for global variable
  ‘mRNA_target’
Undefined global functions or variables:
  mRNA_target miRNAs
* 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
SpidermiRdownload_miRNAvalidate      7.810  0.372  13.636
SpidermiRdownload_miRNAprediction    4.235  1.138   9.286
SpidermiRanalyze_mirna_gene_complnet 3.252  0.183   5.745
* 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-3.5-bioc/meat/SpidermiR.Rcheck/00check.log’
for details.


SpidermiR.Rcheck/00install.out:

* installing *source* package ‘SpidermiR’ ...
** 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 (SpidermiR)

SpidermiR.Rcheck/SpidermiR-Ex.timings:

nameusersystemelapsed
Case_Study1_loading_1_network0.0010.0000.000
Case_Study1_loading_2_network0.0000.0000.001
Case_Study1_loading_3_network0.0010.0000.000
Case_Study1_loading_4_network0.0010.0000.000
Case_Study2_loading_1_network0.0010.0000.001
Case_Study2_loading_2_network0.0010.0000.001
Case_Study2_loading_3_network0.0010.0000.000
SpidermiRanalyze_Community_detection0.0750.0020.078
SpidermiRanalyze_Community_detection_bi0.3740.0040.383
SpidermiRanalyze_Community_detection_net0.0080.0000.008
SpidermiRanalyze_DEnetworkTCGA3.3130.0783.478
SpidermiRanalyze_degree_centrality0.0030.0000.003
SpidermiRanalyze_direct_net0.0270.0010.032
SpidermiRanalyze_direct_subnetwork0.0480.0000.050
SpidermiRanalyze_mirna_gene_complnet3.2520.1835.745
SpidermiRanalyze_mirna_network2.5700.1644.515
SpidermiRanalyze_mirnanet_pharm0.0010.0000.002
SpidermiRanalyze_subnetwork_neigh0.0050.0010.006
SpidermiRdownload_miRNAextra_cir0.0570.0081.684
SpidermiRdownload_miRNAprediction4.2351.1389.286
SpidermiRdownload_miRNAvalidate 7.810 0.37213.636
SpidermiRdownload_net0.4030.0141.645
SpidermiRdownload_pharmacomir0.0140.0010.332
SpidermiRprepare_NET0.5660.0501.996
SpidermiRquery_disease0.0290.0030.505
SpidermiRquery_networks_type0.0160.0010.503
SpidermiRquery_spec_networks0.0520.0010.461
SpidermiRquery_species0.0080.0000.277
SpidermiRvisualize_3Dbarplot0.1550.0050.164
SpidermiRvisualize_BI0.2850.0060.302
SpidermiRvisualize_adj_matrix0.0690.0020.071
SpidermiRvisualize_degree_dist0.0120.0010.013
SpidermiRvisualize_direction0.2310.0110.247
SpidermiRvisualize_mirnanet0.0700.0030.082
SpidermiRvisualize_plot_target1.0850.0031.155