Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-10-19 13:22:04 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 PSMatch on palomino3


To the developers/maintainers of the PSMatch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PSMatch.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 1520/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PSMatch 1.0.0  (landing page)
Laurent Gatto
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/PSMatch
git_branch: RELEASE_3_15
git_last_commit: 7cad135
git_last_commit_date: 2022-04-26 12:21:50 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / 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: PSMatch
Version: 1.0.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PSMatch.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PSMatch_1.0.0.tar.gz
StartedAt: 2022-10-19 03:05:55 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 03:10:00 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 244.7 seconds
RetCode: 0
Status:   OK  
CheckDir: PSMatch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PSMatch.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PSMatch_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/PSMatch.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PSMatch/DESCRIPTION' ... OK
* this is package 'PSMatch' version '1.0.0'
* 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 'PSMatch' 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
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
PSM                 34.76   1.77   37.16
ConnectedComponents  6.76   0.14    7.05
* 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: OK


Installation output

PSMatch.Rcheck/00install.out

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


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'PSMatch' ...
** using staged installation
** R
** 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
* DONE (PSMatch)

Tests output

PSMatch.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("PSMatch")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

> 
> adj <- Matrix::sparseMatrix(
+     i = c(1, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 8),
+     j = c(1, 2, 3, 4, 3, 4, 5, 6, 6, 7, 7, 1),
+     x = 1,
+     dimnames = list(
+         paste0("p", 1:8),
+         paste0("P", 1:7)))
> 
> cc <- Matrix::sparseMatrix(
+     i = c(1, 2, 3, 3, 4, 4, 5, 5, 6, 6, 6, 7, 7),
+     j = c(1, 2, 3, 4, 3, 4, 5, 6, 5, 6, 7, 6, 7),
+     x = c(2, 1, 2, 2, 2, 2, 1, 1, 1, 2, 1, 1, 2),
+     dimnames = list(
+         paste0("P", 1:7),
+         paste0("P", 1:7)))
> 
> adjMatrices <-
+     S4Vectors::List(
+         Matrix::sparseMatrix(
+                     i = c(1, 2), j = c(1, 1), x = 1,
+                     dimnames = list(c("p1", "p8"),
+                                     "P1")),
+         Matrix::sparseMatrix(
+                     i = 1, j = 1, x = 1,
+                     dimnames = list("p2", "P2")),
+         Matrix::sparseMatrix(
+                     i = c(1, 1, 2, 2),
+                     j = c(1, 2, 1, 2),
+                     x = 1,
+                     dimnames = list(
+                         c("p3", "p4"),
+                         c("P3", "P4"))),
+         Matrix::sparseMatrix(
+                     i = c(1, 1, 2, 2, 3),
+                     j = c(1, 2, 2, 3, 3),
+                     x = 1,
+                     dimnames = list(
+                         c("p5", "p6", "p7"),
+                         c("P5", "P6", "P7"))))
> 
> psmdf <- PSM(data.frame(peptide = paste0("p", c(1, 8, 2, 3, 4, 3, 4, 5, 5, 6, 6, 7)),
+                         protein = rep(colnames(adj), Matrix::colSums(adj))),
+              protein = "protein", peptide = "peptide")
> 
> test_check("PSMatch")
An instance of class ConnectedComponents 
 Number of proteins: 7 
 Number of components: 4 
 Number of components [peptide x peptides]:
  1[1 x 1] 0[1 x n] 1[n x 1] 2[n x n]
reading TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid... DONE!
PSM with 5802 rows and 35 columns.
names(35): sequence spectrumID ... subReplacementResidue subLocation
PSM with 5759 rows and 30 columns.
names(30): spectrumid scan number(s) ... spectrumFile databaseFile
PSM with 10 rows and 6 columns.
names(6): spectrum sequence ... rank score
PSM with 15 rows and 6 columns.
names(6): spectrum sequence ... rank score
PSM with 10 rows and 3 columns.
names(3): spectrum sequence protein
Reduced PSM with 5 rows and 5 columns.
names(5): spectrum sequence ... decoy rank
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 189 ]

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 189 ]
> 
> proc.time()
   user  system elapsed 
  28.23    1.40   29.64 

Example timings

PSMatch.Rcheck/PSMatch-Ex.timings

nameusersystemelapsed
ConnectedComponents6.760.147.05
PSM34.76 1.7737.16
addFragments0.780.000.78
adjacencyMatrix1.690.031.72
calculateFragments0.040.030.07
describeProteins0.850.050.89
filterPSMs0.340.010.36
getAminoAcids000
getAtomicMass000