Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:07:17 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SRAdb on palomino4


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? 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 1902/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRAdb 1.59.0  (landing page)
Jack Zhu
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/SRAdb
git_branch: master
git_last_commit: fd18c9a
git_last_commit_date: 2022-04-26 11:04:40 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SRAdb
Version: 1.59.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SRAdb_1.59.0.tar.gz
StartedAt: 2022-06-24 06:11:15 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 06:12:24 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 68.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SRAdb.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SRAdb_1.59.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SRAdb.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.59.0'
* 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 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 sizes of PDF files under 'inst/doc' ... 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
  'F:/biocbuild/bbs-3.16-bioc/meat/SRAdb.Rcheck/00check.log'
for details.



Installation output

SRAdb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/SRAdb_1.59.0.tar.gz && rm -rf SRAdb.buildbin-libdir && mkdir SRAdb.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SRAdb.buildbin-libdir SRAdb_1.59.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL SRAdb_1.59.0.zip && rm SRAdb_1.59.0.tar.gz SRAdb_1.59.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  555k  100  555k    0     0  6029k      0 --:--:-- --:--:-- --:--:-- 6103k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'SRAdb' as SRAdb_1.59.0.zip
* DONE (SRAdb)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'SRAdb' successfully unpacked and MD5 sums checked

Tests output


Example timings

SRAdb.Rcheck/SRAdb-Ex.timings

nameusersystemelapsed
IGVclear000
IGVcollapse000
IGVgenome000
IGVgoto000
IGVload000
IGVsession000
IGVsnapshot000
IGVsocket000
IGVsort000
SRAdb-package0.130.000.15
ascpR000
ascpSRA000
colDescriptions0.020.000.01
entityGraph0.010.000.02
getFASTQfile000
getFASTQinfo000
getSRA0.040.000.03
getSRAdbFile000
getSRAfile000
getSRAinfo000
listSRAfile000
sraConvert0.020.000.02
sraGraph0.330.020.34
startIGV000