Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:07:24 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 RpsiXML on palomino3


To the developers/maintainers of the RpsiXML package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RpsiXML.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 1698/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RpsiXML 2.38.0  (landing page)
Jitao David Zhang
Snapshot Date: 2022-05-17 13:55:01 -0400 (Tue, 17 May 2022)
git_url: https://git.bioconductor.org/packages/RpsiXML
git_branch: RELEASE_3_15
git_last_commit: c2e1b0f
git_last_commit_date: 2022-04-26 11:01:44 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RpsiXML
Version: 2.38.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RpsiXML.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RpsiXML_2.38.0.tar.gz
StartedAt: 2022-05-18 03:17:45 -0400 (Wed, 18 May 2022)
EndedAt: 2022-05-18 03:20:15 -0400 (Wed, 18 May 2022)
EllapsedTime: 150.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RpsiXML.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RpsiXML.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RpsiXML_2.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RpsiXML/DESCRIPTION' ... OK
* this is package 'RpsiXML' version '2.38.0'
* 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 'RpsiXML' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
See 'F:/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck/00install.out' for details.
* 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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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 WARNING
See
  'F:/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck/00check.log'
for details.



Installation output

RpsiXML.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RpsiXML
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RpsiXML' ...
** 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
Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package can be loaded from final location
Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (RpsiXML)

Tests output

RpsiXML.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(RpsiXML)
Loading required package: XML
Warning message:
Package 'RpsiXML' is deprecated and will be removed from Bioconductor
  version 3.16 
> 
> test_check("RpsiXML")
1 Entries found
Parsing entry 1 
  Parsing experiments: .........
  Parsing interactors:

  14% ======>
  29% ============>
  43% =================>
  57% =======================>
  71% ============================>
  86% ==================================>
  100% ========================================>
  Parsing interactions:
......
1 Entries found
Parsing entry 1 
  Parsing experiments: ...
  Parsing interactors:

  14% ======>
  29% ============>
  43% =================>
  57% =======================>
  71% ============================>
  86% ==================================>
  100% ========================================>
  Parsing interactions:
.....
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  6% ==>
  12% =====>
  19% ========>
  25% ==========>
  31% ============>
  38% ===============>
  44% ==================>
  50% ====================>
  56% ======================>
  62% =========================>
  69% ============================>
  75% ==============================>
  81% ================================>
  88% ===================================>
  94% ======================================>
  100% ========================================>
  Parsing interactions:
.................
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  3% =>
  6% ==>
  10% ====>
  13% =====>
  16% ======>
  19% ========>
  23% =========>
  26% ==========>
  29% ============>
  32% =============>
  35% ==============>
  39% ================>
  42% =================>
  45% ==================>
  48% ===================>
  52% =====================>
  55% ======================>
  58% =======================>
  61% ========================>
  65% ==========================>
  68% ===========================>
  71% ============================>
  74% ==============================>
  77% ===============================>
  81% ================================>
  84% ==================================>
  87% ===================================>
  90% ====================================>
  94% ======================================>
  97% =======================================>
  100% ========================================>
  Parsing interactions:
.............................................................................................
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  3% =>
  6% ==>
  10% ====>
  13% =====>
  16% ======>
  19% ========>
  23% =========>
  26% ==========>
  29% ============>
  32% =============>
  35% ==============>
  39% ================>
  42% =================>
  45% ==================>
  48% ===================>
  52% =====================>
  55% ======================>
  58% =======================>
  61% ========================>
  65% ==========================>
  68% ===========================>
  71% ============================>
  74% ==============================>
  77% ===============================>
  81% ================================>
  84% ==================================>
  87% ===================================>
  90% ====================================>
  94% ======================================>
  97% =======================================>
  100% ========================================>
  Parsing interactions:
.............................................................................................
1 Entries found
Parsing entry 1 
  Parsing experiments: 
  Parsing interactors:

  3% =>
  5% ==>
  8% ===>
  10% ====>
  13% =====>
  15% ======>
  18% =======>
  20% ========>
  23% =========>
  25% ==========>
  28% ===========>
  30% ============>
  33% =============>
  35% ==============>
  38% ===============>
  40% ================>
  43% =================>
  45% ==================>
  48% ===================>
  50% ====================>
  53% =====================>
  55% ======================>
  58% =======================>
  60% ========================>
  63% =========================>
  65% ==========================>
  68% ===========================>
  70% ============================>
  73% =============================>
  75% ==============================>
  78% ===============================>
  80% ================================>
  83% =================================>
  86% ==================================>
  88% ===================================>
  91% ====================================>
  93% =====================================>
  96% ======================================>
  98% =======================================>
  100% ========================================>
  Parsing interactions:
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
141 Entries found
Parsing entry 1 
  Parsing experiments: 
  Parsing interactors:

  50% ====================>
  100% ========================================>
  Parsing interactions:
.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  18.00    0.65   18.67 

Example timings

RpsiXML.Rcheck/RpsiXML-Ex.timings

nameusersystemelapsed
availableXrefs0.060.000.06
bait0.030.020.05
buildPCHypergraph1.430.011.54
complexName1.360.131.49
complexes1.350.091.44
eListHandler0.010.000.01
getAbstractByPMID0.360.020.81
graphSpeciesConverter2.140.032.25
interactionType0.050.000.05
interactions0.060.000.06
interactorInfo0.060.000.06
interactors1.160.021.17
null2na000
parsePsimi25Interaction1.250.031.28
psimi25Complex-class000
psimi25ComplexEntry-class000
psimi25Experiment-class000
psimi25Graph-class000
psimi25Hypergraph-class0.970.010.99
psimi25Hypergraph2GraphNEL000
psimi25Interaction-class000
psimi25InteractionEntry-class000
psimi25Interactor-class000
psimi25Source-class000
psimi25XML2Graph1.740.081.82
separateXMLDataByExpt0.850.020.86
translateID2.870.062.94
uniprot000
validatePSIMI25000