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CHECK report for annotate on tokay1

This page was generated on 2020-12-01 11:57:52 -0500 (Tue, 01 Dec 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE annotate PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 61/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.68.0
Bioconductor Package Maintainer
Snapshot Date: 2020-11-30 14:42:56 -0500 (Mon, 30 Nov 2020)
URL: https://git.bioconductor.org/packages/annotate
Branch: RELEASE_3_12
Last Commit: 98cdb12
Last Changed Date: 2020-10-27 10:21:39 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annotate
Version: 1.68.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotate.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annotate_1.68.0.tar.gz
StartedAt: 2020-12-01 00:23:20 -0500 (Tue, 01 Dec 2020)
EndedAt: 2020-12-01 00:27:30 -0500 (Tue, 01 Dec 2020)
EllapsedTime: 250.0 seconds
RetCode: 1
Status:  ERROR  
CheckDir: annotate.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annotate.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings annotate_1.68.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/annotate.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.68.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'annotate' 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 ... OK
* 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 ... 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
chrCats        11.42   0.02   11.44
pm.getabst      4.25   0.00    5.26
pm.titles       4.14   0.02    5.18
accessionToUID  2.98   0.08    6.33
blastSequences  0.13   0.00   21.03
** running examples for arch 'x64' ... ERROR
Running examples in 'annotate-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blastSequences
> ### Title: Run a blast query to NCBI for either a string or an entrez gene
> ###   ID and then return a series of MultipleAlignment objects.
> ### Aliases: blastSequences
> 
> ### ** Examples
> 
> 
> ## x can be an entrez gene ID
> blastSequences(17702, timeout=40, as="data.frame")
estimated response time 16 seconds
elapsed time 17 seconds
Error in curl::curl_fetch_memory(url, handle = handle) : 
  schannel: next InitializeSecurityContext failed: SEC_E_MESSAGE_ALTERED (0x8009030F) - The message or signature supplied for verification has been altered
Calls: blastSequences ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'annotate_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'annotate_unit_tests.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: 1 ERROR
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/annotate.Rcheck/00check.log'
for details.


Installation output

annotate.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/annotate_1.68.0.tar.gz && rm -rf annotate.buildbin-libdir && mkdir annotate.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annotate.buildbin-libdir annotate_1.68.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL annotate_1.68.0.zip && rm annotate_1.68.0.tar.gz annotate_1.68.0.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  769k  100  769k    0     0  2693k      0 --:--:-- --:--:-- --:--:-- 2730k

install for i386

* installing *source* package 'annotate' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'annotate'
    finding HTML links ... done
    ACCNUMStats                             html  
    GO2heatmap                              html  
    GOmnplot                                html  
    HTMLPage-class                          html  
    LL2homology                             html  
    PMIDAmat                                html  
    PWAmat                                  html  
    UniGeneQuery                            html  
    accessionToUID                          html  
    annPkgName                              html  
    annotate-defunct                        html  
    aqListGOIDs                             html  
    blastSequences                          html  
    buildChromLocation                      html  
    buildPubMedAbst                         html  
    chrCats                                 html  
    chromLocation-class                     html  
    compatibleVersions                      html  
    dropECode                               html  
    entrezGeneByID                          html  
    entrezGeneQuery                         html  
    filterGOByOntology                      html  
    findNeighbors                           html  
    genbank                                 html  
    getAnnMap                               html  
    getEvidence                             html  
    getGOTerm                               html  
    getOntology                             html  
    getPMInfo                               html  
    getSYMBOL                               html  
    getSeq4Acc                              html  
    getTDRows                               html  
    hasGOannote                             html  
    hgByChroms                              html  
    hgCLengths                              html  
    hgu95AProbLocs                          html  
    hgu95Achroloc                           html  
    hgu95Achrom                             html  
    hgu95All                                html  
    hgu95Asym                               html  
    homoData-class                          html  
    htmlpage                                html  
    isValidkey                              html  
    makeAnchor                              html  
    mapOrgs                                 html  
    organism                                html  
    p2LL                                    html  
    pm.abstGrep                             html  
    pm.getabst                              html  
    pm.titles                               html  
    pmAbst2HTML                             html  
    pmid2MIAME                              html  
    pmidQuery                               html  
    pubMedAbst-class                        html  
    pubmed                                  html  
    readGEOAnn                              html  
    serializeEnv                            html  
    setRepository                           html  
    updateSymbolsToValidKeys                html  
    usedChromGenes                          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 'annotate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotate' as annotate_1.68.0.zip
* DONE (annotate)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'annotate' successfully unpacked and MD5 sums checked

Tests output

annotate.Rcheck/tests_i386/annotate_unit_tests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("annotate")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: org.Hs.eg.db

'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Tue Dec 01 00:27:17 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
annotate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.82    0.40    6.21 

annotate.Rcheck/tests_x64/annotate_unit_tests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("annotate")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: org.Hs.eg.db

'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Tue Dec 01 00:27:23 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
annotate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.96    0.37    6.34 

Example timings

annotate.Rcheck/examples_i386/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.480.081.57
GO2heatmap0.120.010.14
GOmnplot0.070.000.06
HTMLPage-class000
LL2homology000
PMIDAmat0.080.030.20
PWAmat1.780.131.91
UniGeneQuery000
accessionToUID2.980.086.33
annPkgName000
aqListGOIDs0.310.010.33
blastSequences 0.13 0.0021.03
buildChromLocation0.590.050.64
buildPubMedAbst0.080.000.73
chrCats11.42 0.0211.44
chromLocation-class0.780.010.80
compatibleVersions0.050.000.04
dropECode0.030.020.05
entrezGeneByID000
entrezGeneQuery000
filterGOByOntology0.060.010.08
findNeighbors0.010.000.17
genbank2.850.033.34
getAnnMap0.050.071.36
getEvidence0.060.010.08
getGOTerm0.350.000.36
getOntology0.060.000.06
getPMInfo0.550.021.05
getSYMBOL0.140.000.21
getSeq4Acc0.000.000.19
hasGOannote0.030.000.03
hgByChroms0.010.010.03
hgCLengths0.000.020.02
hgu95Achroloc0.100.030.13
hgu95Achrom0.110.000.11
hgu95All0.090.010.11
hgu95Asym0.090.050.14
homoData-class000
htmlpage0.040.000.03
isValidkey000
makeAnchor000
organism1.420.011.44
p2LL000
pm.abstGrep3.500.004.48
pm.getabst4.250.005.26
pm.titles4.140.025.18
pmAbst2HTML0.130.000.57
pmid2MIAME000
pmidQuery000
pubMedAbst-class0.140.000.75
pubmed0.140.000.44
readGEOAnn000
serializeEnv0.020.000.02
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.090.010.11

annotate.Rcheck/examples_x64/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.580.101.67
GO2heatmap0.170.000.17
GOmnplot0.070.000.08
HTMLPage-class000
LL2homology000
PMIDAmat0.140.000.14
PWAmat2.200.062.26
UniGeneQuery000
accessionToUID2.130.064.07
annPkgName000
aqListGOIDs0.190.000.18