##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PSMatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PSMatch_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PSMatch.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSMatch/DESCRIPTION’ ... OK
* this is package ‘PSMatch’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... 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 code 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 ... NOTE
Namespace in Imports field not imported from: ‘IRanges’
  All declared Imports should be used.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'labelFragments.Rd':
  ‘[MsCoreUtils:matching]{MsCoreUtils::common()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PSM.Rd: DataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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                 33.905  0.476  34.927
ConnectedComponents  6.727  0.295   7.068
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/PSMatch.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PSMatch
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘PSMatch’ ...
** this is package ‘PSMatch’ version ‘1.12.0’
** 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)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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("vdiffr")
> library("PSMatch")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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 proteins]:
  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 7 columns.
names(7): spectrum sequence ... score fdr
PSM with 15 rows and 7 columns.
names(7): spectrum sequence ... score fdr
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 3 | PASS 207 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test_plotSpectraPTM.R:23:5', 'test_plotSpectraPTM.R:53:5',
  'test_plotSpectraPTM.R:114:5'

[ FAIL 0 | WARN 13 | SKIP 3 | PASS 207 ]
Deleting unused snapshots:
• plotSpectraPTM/one-ptm-deltamz-true.svg
> 
> proc.time()
   user  system elapsed 
 29.129   1.381  30.709