Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2021-06-19 12:06:11 -0400 (Sat, 19 Jun 2021).

CHECK results for SRAdb on riesling1

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 1796/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRAdb 1.55.0  (landing page)
Jack Zhu
Snapshot Date: 2021-06-18 14:50:08 -0400 (Fri, 18 Jun 2021)
URL: https://git.bioconductor.org/packages/SRAdb
Branch: master
Last Commit: bcaa3a3
Last Changed Date: 2021-05-19 11:45:18 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SRAdb
Version: 1.55.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SRAdb_1.55.0.tar.gz
StartedAt: 2021-06-19 02:18:37 -0400 (Sat, 19 Jun 2021)
EndedAt: 2021-06-19 02:20:24 -0400 (Sat, 19 Jun 2021)
EllapsedTime: 106.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SRAdb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SRAdb_1.55.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/SRAdb.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SRAdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SRAdb' version '1.55.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbuild/bbs-3.14-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/3.14/bioc/src/contrib/SRAdb_1.55.0.tar.gz && rm -rf SRAdb.buildbin-libdir && mkdir SRAdb.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SRAdb.buildbin-libdir SRAdb_1.55.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SRAdb_1.55.0.zip && rm SRAdb_1.55.0.tar.gz SRAdb_1.55.0.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  2709k      0 --:--:-- --:--:-- --:--:-- 2709k

install for i386

* installing *source* package 'SRAdb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SRAdb'
    finding HTML links ... done
    IGVclear                                html  
    IGVcollapse                             html  
    IGVgenome                               html  
    IGVgoto                                 html  
    IGVload                                 html  
    IGVsession                              html  
    IGVsnapshot                             html  
    IGVsocket                               html  
    IGVsort                                 html  
    SRAdb-package                           html  
    ascpR                                   html  
    ascpSRA                                 html  
    colDescriptions                         html  
    entityGraph                             html  
    getFASTQfile                            html  
    getFASTQinfo                            html  
    getSRA                                  html  
    getSRAdbFile                            html  
    getSRAfile                              html  
    getSRAinfo                              html  
    listSRAfile                             html  
    sraConvert                              html  
    sraGraph                                html  
    startIGV                                html  
** 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

install for x64

* installing *source* package 'SRAdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SRAdb' as SRAdb_1.55.0.zip
* DONE (SRAdb)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'SRAdb' successfully unpacked and MD5 sums checked

Tests output


Example timings

SRAdb.Rcheck/examples_i386/SRAdb-Ex.timings

nameusersystemelapsed
IGVclear000
IGVcollapse000
IGVgenome000
IGVgoto000
IGVload000
IGVsession000
IGVsnapshot000
IGVsocket000
IGVsort000
SRAdb-package0.090.000.10
ascpR000
ascpSRA000
colDescriptions0.010.000.02
entityGraph0.020.000.01
getFASTQfile000
getFASTQinfo000
getSRA0.030.000.03
getSRAdbFile000
getSRAfile000
getSRAinfo0.020.000.02
listSRAfile000
sraConvert000
sraGraph0.210.010.23
startIGV000

SRAdb.Rcheck/examples_x64/SRAdb-Ex.timings

nameusersystemelapsed
IGVclear000
IGVcollapse000
IGVgenome000
IGVgoto000
IGVload000
IGVsession000
IGVsnapshot000
IGVsocket000
IGVsort0.000.020.02
SRAdb-package0.080.000.08
ascpR000
ascpSRA000
colDescriptions0.030.000.03
entityGraph000
getFASTQfile000
getFASTQinfo000
getSRA0.020.000.02
getSRAdbFile000
getSRAfile000
getSRAinfo000
listSRAfile000
sraConvert000
sraGraph0.240.010.25
startIGV000