Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-06-18 14:06:00 -0400 (Fri, 18 Jun 2021).

CHECK results for SRAdb on nebbiolo1

To the developers/maintainers of the SRAdb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SRAdb.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1840/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRAdb 1.54.0  (landing page)
Jack Zhu
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/SRAdb
Branch: RELEASE_3_13
Last Commit: d4df032
Last Changed Date: 2021-05-19 11:45:18 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SRAdb
Version: 1.54.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SRAdb.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SRAdb_1.54.0.tar.gz
StartedAt: 2021-06-17 13:45:53 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 13:46:38 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 44.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SRAdb.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SRAdb.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SRAdb_1.54.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/SRAdb.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SRAdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SRAdb’ version ‘1.54.0’
* 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 ‘SRAdb’ 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 ... NOTE
The following files look like leftovers:
  ‘SRAdb/SRAdb-package.Rd’
Please remove them from your package.
* 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
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘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
.socketWrite: no visible global function definition for ‘write.socket’
.socketWrite: no visible global function definition for ‘read.socket’
IGVsocket: no visible global function definition for ‘make.socket’
colDescriptions: no visible global function definition for ‘dbGetQuery’
entityGraph: no visible global function definition for ‘na.omit’
entityGraph: no visible global function definition for ‘new’
entityGraph : <anonymous>: no visible global function definition for
  ‘addEdge’
getFASTQfile: no visible global function definition for ‘download.file’
getFASTQinfo: no visible global function definition for ‘dbGetQuery’
getSRA: no visible global function definition for ‘dbGetQuery’
getSRAdbFile: no visible global function definition for ‘download.file’
getSRAdbFile: no visible global function definition for ‘dbConnect’
getSRAdbFile: no visible global function definition for ‘SQLite’
getSRAdbFile: no visible global function definition for ‘dbGetQuery’
getSRAdbFile: no visible global function definition for ‘dbDisconnect’
getSRAfile: no visible global function definition for ‘download.file’
getSRAinfo: no visible global function definition for ‘na.omit’
sraConvert: no visible global function definition for ‘dbGetQuery’
startIGV: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  SQLite addEdge browseURL dbConnect dbDisconnect dbGetQuery
  download.file make.socket na.omit new read.socket write.socket
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "download.file", "make.socket",
             "read.socket", "write.socket")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/SRAdb.Rcheck/00check.log’
for details.



Installation output

SRAdb.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SRAdb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘SRAdb’ ...
** using staged installation
** R
** 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 (SRAdb)

Tests output


Example timings

SRAdb.Rcheck/SRAdb-Ex.timings

nameusersystemelapsed
IGVclear0.0010.0000.001
IGVcollapse000
IGVgenome0.0000.0010.000
IGVgoto0.0000.0010.001
IGVload0.0000.0000.001
IGVsession0.0000.0020.002
IGVsnapshot0.0000.0010.001
IGVsocket000
IGVsort000
SRAdb-package0.1150.0040.127
ascpR000
ascpSRA000
colDescriptions0.0260.0030.029
entityGraph0.0190.0010.019
getFASTQfile0.0010.0000.001
getFASTQinfo000
getSRA0.0330.0070.040
getSRAdbFile0.0010.0000.001
getSRAfile0.0030.0010.003
getSRAinfo0.0030.0000.003
listSRAfile0.0010.0000.001
sraConvert0.0010.0030.005
sraGraph0.2920.0080.300
startIGV000