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###
### 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PSMatch.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSMatch/DESCRIPTION’ ... OK
* this is package ‘PSMatch’ 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 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 ... 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 ... ERROR
Running examples in ‘PSMatch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PSM
> ### Title: A class for peptide-spectrum matches
> ### Aliases: PSM PSM-class reducePSMs readPSMs psmVariables PSM,character
> ###   PSM,data.frame PSM,PSM reduced reduced<- adjacencyMatrix,PSM-method
> 
> ### ** Examples
> 
> 
> ## ---------------------------------
> ## Example with a single mzid file
> ## ---------------------------------
> 
> f <- msdata::ident(full.names = TRUE, pattern = "TMT")
> basename(f)
[1] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"
> 
> ## mzR parser (default)
> psm <- PSM(f)
> psm
PSM with 5802 rows and 35 columns.
names(35): sequence spectrumID ... subReplacementResidue subLocation
> 
> ## PSM variables
> psmVariables(psm)
        spectrum          peptide          protein            decoy 
    "spectrumID"       "sequence" "DatabaseAccess"        "isDecoy" 
            rank            score              fdr 
          "rank"               NA               NA 
> 
> ## mzID parser
> psm_mzid <- PSM(f, parser = "mzID")
Loading required namespace: mzID
reading TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid...Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
 DONE!
> psm_mzid
PSM with 5759 rows and 30 columns.
names(30): spectrumid scan number(s) ... spectrumFile databaseFile
> 
> ## different PSM variables
> psmVariables(psm_mzid)
    spectrum      peptide      protein        decoy         rank        score 
"spectrumid"     "pepseq"  "accession"    "isdecoy"       "rank"           NA 
         fdr 
          NA 
> 
> ## Reducing the PSM data
> (i <- which(duplicated(psm$spectrumID))[1:2])
[1]  9 24
> (i <- which(psm$spectrumID %in% psm$spectrumID[i]))
[1]  8  9 23 24 25 26
> psm2 <- psm[i, ]
> reduced(psm2)
[1] NA
> 
> ## Peptide sequence CIDRARHVEVQIFGDGKGRVVALGERDCSLQRR with
> ## Carbamidomethyl modifications at positions 1 and 28.
> DataFrame(psm2[, c("sequence", "spectrumID", "modName", "modLocation")])
DataFrame with 6 rows and 4 columns
       sequence    spectrumID       modName modLocation
    <character>   <character>   <character>   <integer>
1 CIDRARHVEV... controller... Carbamidom...           1
2 CIDRARHVEV... controller... Carbamidom...          28
3 KCNQCLKVAC... controller... Carbamidom...           2
4 KCNQCLKVAC... controller... Carbamidom...           5
5 KCNQCLKVAC... controller... Carbamidom...          10
6 KCNQCLKVAC... controller... Carbamidom...          15
> reduced(psm2) <- FALSE
> reduced(psm2)
[1] FALSE
> 
> ## uses by default the spectrum PSM variable, as defined during
> ## the construction - see psmVariables()
> rpsm2 <- reducePSMs(psm2)
> rpsm2
Reduced PSM with 2 rows and 35 columns.
names(35): sequence spectrumID ... subReplacementResidue subLocation
> DataFrame(rpsm2[, c("sequence", "spectrumID", "modName", "modLocation")])
DataFrame with 2 rows and 4 columns
                                                   sequence    spectrumID
                                                <character>   <character>
controllerType=0 controllerNumber=1 scan=5490 KCNQCLKVAC... controller...
controllerType=0 controllerNumber=1 scan=6518 CIDRARHVEV... controller...
                                                    modName   modLocation
                                                <character> <IntegerList>
controllerType=0 controllerNumber=1 scan=5490 Carbamidom...    2,5,10,...
controllerType=0 controllerNumber=1 scan=6518 Carbamidom...          1,28
> reduced(rpsm2)
[1] TRUE
> 
> ## ---------------------------------
> ## Multiple mzid files
> ## ---------------------------------
> 
> library(rpx)
> PXD022816 <- PXDataset("PXD022816")
Loading PXD022816 from cache.
> PXD022816
Project PXD022816 with 32 files
 Resource ID BFC36 in cache in /Users/biocbuild/Library/Caches/org.R-project.R/R/rpx.
 [1] 'QEP2LC6_HeLa_50ng_251120_01-calib.mzID.gz' ... [32] 'checksum.txt'
 Use 'pxfiles(.)' to see all files.
> 
> (mzids <- pxget(PXD022816, grep("mzID", pxfiles(PXD022816))[1:2]))
Project PXD022816 files (32):
 [local]  QEP2LC6_HeLa_50ng_251120_01-calib.mzID.gz
 [local]  QEP2LC6_HeLa_50ng_251120_01-calib.mzML
 [remote] QEP2LC6_HeLa_50ng_251120_01.raw
 [local]  QEP2LC6_HeLa_50ng_251120_02-calib.mzID.gz
 [local]  QEP2LC6_HeLa_50ng_251120_02-calib.mzML
 [remote] QEP2LC6_HeLa_50ng_251120_02.raw
 [remote] QEP2LC6_HeLa_50ng_251120_03-calib.mzID.gz
 [remote] QEP2LC6_HeLa_50ng_251120_03-calib.mzML
 [remote] QEP2LC6_HeLa_50ng_251120_03.raw
 [remote] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
 ...
Loading QEP2LC6_HeLa_50ng_251120_01-calib.mzID.gz from cache.
Error in fix_issue_17(x) : Can't access URL(s):
 ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD022816/QEP2LC6_HeLa_50ng_251120_02-calib.mzID.gz
 ftp://ftp.pride.ebi.ac.uk/pride-archive/2021/03/PXD022816/QEP2LC6_HeLa_50ng_251120_02-calib.mzID.gz
Calls: pxget ... pxget -> .local -> pxget1 -> get_url -> fix_issue_17
Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/PSMatch.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PSMatch
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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("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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, 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 0 | PASS 193 ]

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 193 ]
> 
> proc.time()
   user  system elapsed 
 31.208   1.103  32.372