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BioC experimental data: CHECK report for curatedMetagenomicData on malbec1

This page was generated on 2017-04-15 16:49:49 -0400 (Sat, 15 Apr 2017).

Package 65/310HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedMetagenomicData 1.0.4
Lucas Schiffer
Snapshot Date: 2017-04-15 09:20:05 -0400 (Sat, 15 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_4/experiment/pkgs/curatedMetagenomicData
Last Changed Rev: 4011 / Revision: 4141
Last Changed Date: 2016-12-12 14:32:16 -0500 (Mon, 12 Dec 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedMetagenomicData
Version: 1.0.4
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings curatedMetagenomicData_1.0.4.tar.gz
StartedAt: 2017-04-15 10:48:12 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 11:05:19 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 1027.3 seconds
RetCode: 0
Status:  OK 
CheckDir: curatedMetagenomicData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings curatedMetagenomicData_1.0.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘curatedMetagenomicData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedMetagenomicData’ version ‘1.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘dplyr’ ‘phyloseq’ ‘Biobase’ ‘ExperimentHub’ ‘AnnotationHub’
  ‘magrittr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘curatedMetagenomicData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocInstaller’
A package should be listed in only one of these fields.
* 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 ... NOTE
prepare_Rd: TettAJ_2016.genefamilies_relab.Rd:10-12: Dropping empty section \source
prepare_Rd: TettAJ_2016.marker_abundance.Rd:10-12: Dropping empty section \source
prepare_Rd: TettAJ_2016.marker_presence.Rd:10-12: Dropping empty section \source
prepare_Rd: TettAJ_2016.metaphlan_bugs_list.Rd:10-12: Dropping empty section \source
prepare_Rd: TettAJ_2016.pathabundance_relab.Rd:10-12: Dropping empty section \source
prepare_Rd: TettAJ_2016.pathcoverage.Rd:10-12: Dropping empty section \source
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                          user system elapsed
NielsenHB_2014.genefamilies_relab      248.412  5.968 255.510
LeChatelierE_2013.genefamilies_relab   155.408  5.848 161.616
KarlssonFH_2013.genefamilies_relab      77.052  2.500  79.697
OhJ_2014.genefamilies_relab             43.004 13.772  56.912
HMP_2012.genefamilies_relab             54.084  2.440  56.722
QinJ_2012.genefamilies_relab            26.608  6.048  33.489
NielsenHB_2014.marker_abundance         26.784  1.216  28.368
QinN_2014.genefamilies_relab            17.316  6.636  25.297
LeChatelierE_2013.marker_abundance      20.360  0.560  21.116
NielsenHB_2014.marker_presence          19.560  1.052  20.839
ZellerG_2014.genefamilies_relab         14.608  4.692  19.540
LomanNJ_2013_Hi.genefamilies_relab      11.120  0.340  11.573
LeChatelierE_2013.marker_presence       10.492  0.044  10.721
KarlssonFH_2013.marker_abundance         6.176  0.260   6.630
Obregon_TitoAJ_2015.genefamilies_relab   4.976  1.176   7.577
* 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-data-experiment/meat/curatedMetagenomicData.Rcheck/00check.log’
for details.

curatedMetagenomicData.Rcheck/00install.out:

* installing *source* package ‘curatedMetagenomicData’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (curatedMetagenomicData)

curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings:

nameusersystemelapsed
ExpressionSet2phyloseq1.0440.0362.010
HMP_2012.genefamilies_relab54.084 2.44056.722
HMP_2012.marker_abundance4.4480.0724.747
HMP_2012.marker_presence4.1520.2164.432
HMP_2012.metaphlan_bugs_list0.1000.0080.160
HMP_2012.pathabundance_relab0.5120.0080.670
HMP_2012.pathcoverage0.2040.0080.280
KarlssonFH_2013.genefamilies_relab77.052 2.50079.697
KarlssonFH_2013.marker_abundance6.1760.2606.630
KarlssonFH_2013.marker_presence4.2960.0244.492
KarlssonFH_2013.metaphlan_bugs_list0.1080.0040.189
KarlssonFH_2013.pathabundance_relab0.5960.0080.654
KarlssonFH_2013.pathcoverage0.2440.0040.298
LeChatelierE_2013.genefamilies_relab155.408 5.848161.616
LeChatelierE_2013.marker_abundance20.360 0.56021.116
LeChatelierE_2013.marker_presence10.492 0.04410.721
LeChatelierE_2013.metaphlan_bugs_list0.2160.0080.389
LeChatelierE_2013.pathabundance_relab0.2800.0040.331
LeChatelierE_2013.pathcoverage0.2560.0360.338
LomanNJ_2013_Hi.genefamilies_relab11.120 0.34011.573
LomanNJ_2013_Hi.marker_abundance1.1200.0401.319
LomanNJ_2013_Hi.marker_presence0.8440.0480.943
LomanNJ_2013_Hi.metaphlan_bugs_list0.1400.0080.201
LomanNJ_2013_Hi.pathabundance_relab0.1880.0080.240
LomanNJ_2013_Hi.pathcoverage0.1720.0120.232
LomanNJ_2013_Mi.genefamilies_relab2.2800.0682.412
LomanNJ_2013_Mi.marker_abundance0.9760.0121.033
LomanNJ_2013_Mi.marker_presence0.3120.0000.433
LomanNJ_2013_Mi.metaphlan_bugs_list0.1280.0000.179
LomanNJ_2013_Mi.pathabundance_relab0.1400.0000.185
LomanNJ_2013_Mi.pathcoverage0.1480.0000.196
NielsenHB_2014.genefamilies_relab248.412 5.968255.510
NielsenHB_2014.marker_abundance26.784 1.21628.368
NielsenHB_2014.marker_presence19.560 1.05220.839
NielsenHB_2014.metaphlan_bugs_list0.2160.0000.411
NielsenHB_2014.pathabundance_relab0.3320.1200.533
NielsenHB_2014.pathcoverage0.3520.1080.551
Obregon_TitoAJ_2015.genefamilies_relab4.9761.1767.577
Obregon_TitoAJ_2015.marker_abundance1.0000.1921.344
Obregon_TitoAJ_2015.marker_presence0.7160.1480.928
Obregon_TitoAJ_2015.metaphlan_bugs_list0.1440.0000.194
Obregon_TitoAJ_2015.pathabundance_relab0.1960.0000.252
Obregon_TitoAJ_2015.pathcoverage0.6160.0360.733
OhJ_2014.genefamilies_relab43.00413.77256.912
OhJ_2014.marker_abundance2.3400.9683.497
OhJ_2014.marker_presence2.0920.9283.098
OhJ_2014.metaphlan_bugs_list0.1760.0040.235
OhJ_2014.pathabundance_relab0.6160.2320.896
OhJ_2014.pathcoverage0.6000.5801.229
QinJ_2012.genefamilies_relab26.608 6.04833.489
QinJ_2012.marker_abundance1.8880.8443.096
QinJ_2012.marker_presence1.8280.7243.167
QinJ_2012.metaphlan_bugs_list0.1480.0041.031
QinJ_2012.pathabundance_relab0.4760.1201.354
QinJ_2012.pathcoverage0.3440.1240.514
QinN_2014.genefamilies_relab17.316 6.63625.297
QinN_2014.marker_abundance1.5320.5282.278
QinN_2014.marker_presence1.3080.4081.933
QinN_2014.metaphlan_bugs_list0.1200.0000.167
QinN_2014.pathabundance_relab0.2880.0720.407
QinN_2014.pathcoverage0.3000.0720.425
RampelliS_2015.genefamilies_relab2.6320.4964.138
RampelliS_2015.marker_abundance0.2560.0280.330
RampelliS_2015.marker_presence0.8480.2321.789
RampelliS_2015.metaphlan_bugs_list0.1040.0000.289
RampelliS_2015.pathabundance_relab0.1240.0120.491
RampelliS_2015.pathcoverage0.1680.0080.223
TettAJ_2016.genefamilies_relab2.9400.4763.477
TettAJ_2016.marker_abundance0.2960.0040.363
TettAJ_2016.marker_presence0.2760.0040.325
TettAJ_2016.metaphlan_bugs_list0.1160.0080.175
TettAJ_2016.pathabundance_relab0.1680.0000.227
TettAJ_2016.pathcoverage0.1880.0080.243
ZellerG_2014.genefamilies_relab14.608 4.69219.540
ZellerG_2014.marker_abundance1.0560.3281.612
ZellerG_2014.marker_presence1.0240.3081.610
ZellerG_2014.metaphlan_bugs_list0.1640.0000.240
ZellerG_2014.pathabundance_relab0.3000.0000.365
ZellerG_2014.pathcoverage0.3240.0560.434