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CHECK report for SRAdb on malbec2

This page was generated on 2020-10-17 11:55:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SRAdb PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1727/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRAdb 1.50.0
Jack Zhu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SRAdb
Branch: RELEASE_3_11
Last Commit: fc16df9
Last Changed Date: 2020-04-27 14:21:57 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SRAdb
Version: 1.50.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SRAdb.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SRAdb_1.50.0.tar.gz
StartedAt: 2020-10-17 05:47:51 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:48:55 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 64.2 seconds
RetCode: 0
Status:  OK 
CheckDir: SRAdb.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SRAdb.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SRAdb_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SRAdb.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.50.0’
* 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-3.11-bioc/meat/SRAdb.Rcheck/00check.log’
for details.



Installation output

SRAdb.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SRAdb
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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
IGVclear0.0000.0000.001
IGVcollapse000
IGVgenome0.0010.0000.000
IGVgoto0.0010.0000.000
IGVload0.0000.0010.000
IGVsession0.0000.0030.003
IGVsnapshot000
IGVsocket000
IGVsort000
SRAdb-package0.2070.0030.356
ascpR0.0010.0000.000
ascpSRA000
colDescriptions0.050.000.05
entityGraph0.0340.0000.034
getFASTQfile0.0010.0000.001
getFASTQinfo0.0010.0000.000
getSRA0.0680.0000.067
getSRAdbFile0.0010.0000.001
getSRAfile0.0040.0000.004
getSRAinfo0.0040.0000.004
listSRAfile000
sraConvert0.0150.0000.015
sraGraph0.5770.0080.585
startIGV000