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CHECK report for IMMAN on tokay1

This page was generated on 2021-05-06 12:31:49 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the IMMAN package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 885/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IMMAN 1.10.0  (landing page)
Minoo Ashtiani
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/IMMAN
Branch: RELEASE_3_12
Last Commit: b4cfedb
Last Changed Date: 2020-10-27 11:33:46 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    ERROR  skipped
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: IMMAN
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IMMAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings IMMAN_1.10.0.tar.gz
StartedAt: 2021-05-06 03:48:46 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:53:19 -0400 (Thu, 06 May 2021)
EllapsedTime: 272.4 seconds
RetCode: 1
Status:   ERROR   
CheckDir: IMMAN.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IMMAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings IMMAN_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/IMMAN.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IMMAN/DESCRIPTION' ... OK
* this is package 'IMMAN' version '1.10.0'
* package encoding: UTF-8
* 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 'IMMAN' 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 ... NOTE
IMMAN: no visible binding for global variable 'tem'
IMMAN : <anonymous>: no visible binding for global variable 'tem'
Undefined global functions or variables:
  tem
* 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' ... ERROR
Running examples in 'IMMAN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IMMAN
> ### Title: Interlog protein network reconstruction by Mapping and Mining
> ###   ANalysis
> ### Aliases: IMMAN
> 
> ### ** Examples
> 
> 
> data(FruitFly)
> data(Celegance)
> 
> subFruitFly <- as.character(FruitFly$V1)[1:10]
> subCelegance <- as.character(Celegance$V1)[1:10]
> 
> ProteinLists = list(subFruitFly, subCelegance)
> 
> List1_Species_ID = 7227  # taxonomy ID FruitFly
> List2_Species_ID = 6239  # taxonomy ID Celegance
> 
> Species_IDs  = c(List1_Species_ID, List2_Species_ID)
> 
> identityU = 30
> substitutionMatrix = "BLOSUM62"
> gapOpening = -8
> gapExtension = -8
> NetworkShrinkage = FALSE
> coverage = 1
> BestHit = TRUE
> score_threshold = 400
> STRINGversion="11"
> 
> # Run the IMMAN function for the parameters
> output = IMMAN(ProteinLists, fileNames=NULL, Species_IDs,
+               identityU, substitutionMatrix,
+               gapOpening, gapExtension, BestHit,
+               coverage, NetworkShrinkage,
+               score_threshold, STRINGversion,
+               InputDirectory = getwd())
Step 1/4:Downloading amino acid sequences...
Downloading amino acid sequences of List1
Warning in file(con, "r") :
  InternetOpenUrl failed: 'The operation timed out'
Error in file(con, "r") : cannot open the connection
Calls: IMMAN -> apply -> FUN -> read.fasta -> readLines -> file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'IMMAN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IMMAN
> ### Title: Interlog protein network reconstruction by Mapping and Mining
> ###   ANalysis
> ### Aliases: IMMAN
> 
> ### ** Examples
> 
> 
> data(FruitFly)
> data(Celegance)
> 
> subFruitFly <- as.character(FruitFly$V1)[1:10]
> subCelegance <- as.character(Celegance$V1)[1:10]
> 
> ProteinLists = list(subFruitFly, subCelegance)
> 
> List1_Species_ID = 7227  # taxonomy ID FruitFly
> List2_Species_ID = 6239  # taxonomy ID Celegance
> 
> Species_IDs  = c(List1_Species_ID, List2_Species_ID)
> 
> identityU = 30
> substitutionMatrix = "BLOSUM62"
> gapOpening = -8
> gapExtension = -8
> NetworkShrinkage = FALSE
> coverage = 1
> BestHit = TRUE
> score_threshold = 400
> STRINGversion="11"
> 
> # Run the IMMAN function for the parameters
> output = IMMAN(ProteinLists, fileNames=NULL, Species_IDs,
+               identityU, substitutionMatrix,
+               gapOpening, gapExtension, BestHit,
+               coverage, NetworkShrinkage,
+               score_threshold, STRINGversion,
+               InputDirectory = getwd())
Step 1/4:Downloading amino acid sequences...
Downloading amino acid sequences of List1
Warning in file(con, "r") :
  InternetOpenUrl failed: 'The operation timed out'
Error in file(con, "r") : cannot open the connection
Calls: IMMAN -> apply -> FUN -> read.fasta -> readLines -> file
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Error (test_IMMAN.R:6:2): IMMAN reconstruct the interlog protein network ----
  Error: cannot open the connection
  Backtrace:
      x
   1. \-IMMAN::IMMAN(...) test_IMMAN.R:6:1
   2.   \-base::apply(...)
   3.     \-IMMAN:::FUN(newX[, i], ...)
   4.       \-seqinr::read.fasta(...)
   5.         \-base::readLines(file)
   6.           \-base::file(con, "r")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Error (test_IMMAN.R:6:2): IMMAN reconstruct the interlog protein network ----
  Error: cannot open the connection
  Backtrace:
      x
   1. \-IMMAN::IMMAN(...) test_IMMAN.R:6:1
   2.   \-base::apply(...)
   3.     \-IMMAN:::FUN(newX[, i], ...)
   4.       \-seqinr::read.fasta(...)
   5.         \-base::readLines(file)
   6.           \-base::file(con, "r")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/IMMAN.Rcheck/00check.log'
for details.

Installation output

IMMAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/IMMAN_1.10.0.tar.gz && rm -rf IMMAN.buildbin-libdir && mkdir IMMAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IMMAN.buildbin-libdir IMMAN_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL IMMAN_1.10.0.zip && rm IMMAN_1.10.0.tar.gz IMMAN_1.10.0.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 14733  100 14733    0     0  1181k      0 --:--:-- --:--:-- --:--:-- 1307k

install for i386

* installing *source* package 'IMMAN' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IMMAN'
    finding HTML links ... done
    Celegance                               html  
    FruitFly                                html  
    H.sapiens                               html  
    IMMAN                                   html  
    R.norvegicus                            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 'IMMAN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IMMAN' as IMMAN_1.10.0.zip
* DONE (IMMAN)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'IMMAN' successfully unpacked and MD5 sums checked

Tests output

IMMAN.Rcheck/tests_i386/testthat.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> library(testthat)
> library(IMMAN)
> 
> test_check("IMMAN")
== Failed tests ================================================================
-- Error (test_IMMAN.R:6:2): IMMAN reconstruct the interlog protein network ----
Error: cannot open the connection
Backtrace:
    x
 1. \-IMMAN::IMMAN(...) test_IMMAN.R:6:1
 2.   \-base::apply(...)
 3.     \-IMMAN:::FUN(newX[, i], ...)
 4.       \-seqinr::read.fasta(...)
 5.         \-base::readLines(file)
 6.           \-base::file(con, "r")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted

IMMAN.Rcheck/tests_x64/testthat.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> library(testthat)
> library(IMMAN)
> 
> test_check("IMMAN")
== Failed tests ================================================================
-- Error (test_IMMAN.R:6:2): IMMAN reconstruct the interlog protein network ----
Error: cannot open the connection
Backtrace:
    x
 1. \-IMMAN::IMMAN(...) test_IMMAN.R:6:1
 2.   \-base::apply(...)
 3.     \-IMMAN:::FUN(newX[, i], ...)
 4.       \-seqinr::read.fasta(...)
 5.         \-base::readLines(file)
 6.           \-base::file(con, "r")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted

Example timings

IMMAN.Rcheck/examples_i386/IMMAN-Ex.timings

nameusersystemelapsed
Celegance000
FruitFly0.020.000.01
H.sapiens000

IMMAN.Rcheck/examples_x64/IMMAN-Ex.timings

nameusersystemelapsed
Celegance0.010.000.02
FruitFly000
H.sapiens000