##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mspms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mspms_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/mspms.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mspms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mspms’ version ‘1.3.1’
* 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 ‘mspms’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.0Mb
* 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 whether startup messages can be suppressed ... 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
log2fc_t_test    128.720  0.880 130.376
plot_heatmap      20.982  0.685  21.779
limma_stats        9.218  0.473   9.740
prepare_diann      7.691  0.156   7.828
prepare_fragpipe   5.669  0.157   5.768
prepare_peaks      5.056  0.103   5.115
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/mspms.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘mspms’ ...
** this is package ‘mspms’ version ‘1.3.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (mspms)

R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(mspms)
> 
> test_check("mspms")
Loading required namespace: QFeatures
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Rows: 2444 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: ","
chr  (6): Protein Accession, Peptide, Used, Candidate, Sample Profile (Ratio...
dbl (25): Protein Group, Protein ID, Quality, Significance, Avg. ppm, Avg. A...
lgl  (1): PTM

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 12 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): quantCols, group, condition
dbl (1): time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Loading required namespace: imputeLCMD
Imputing along margin 2 (samples/columns).
Your row data contain missing values. Please read the relevant
section(s) in the aggregateFeatures manual page regarding the effects
of missing values on data aggregation.

Aggregated: 1/1
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Rows: 3657 Columns: 28
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (6): Protein.Group, Protein.Ids, Stripped.Sequence, Modified.Sequence, ...
dbl (18): Proteotypic, Precursor.Charge, D:\Charlie\conce_mspms\CS_MSPMS_Spe...
lgl  (4): Protein.Names, Genes, First.Protein.Description, All Mapped Genes

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 16 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): quantCols, group, condition
dbl (1): time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Rows: 1847 Columns: 63
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (19): Peptide Sequence, Prev AA, Next AA, Protein, Protein ID, Entry Nam...
dbl (40): Start, End, Peptide Length, CatA_0000_1 Spectral Count, CatA_0000_...
num  (1): Charges
lgl  (3): Gene, Mapped Genes, Mapped Proteins

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 12 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): quantCols, group, condition
dbl (1): time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Rows: 2444 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): Protein Group,Protein ID,Protein Accession,Peptide,Used,Candidate,Q...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 1207 Columns: 68
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (17): Confidence, Annotated Sequence, Master Protein Accessions, Positio...
dbl (48): Peptide Groups Peptide Group ID, Qvality PEP, Qvality q-value, # P...
lgl  (3): Checked, Modifications, Modifications in Master Proteins

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 12 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): quantCols, group, condition
dbl (1): time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Rows: 2444 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: ","
chr  (6): Protein Accession, Peptide, Used, Candidate, Sample Profile (Ratio...
dbl (25): Protein Group, Protein ID, Quality, Significance, Avg. ppm, Avg. A...
lgl  (1): PTM

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 12 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): quantCols, group, condition
dbl (1): time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Rows: 1555 Columns: 18
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (2): peptide, proteins
dbl (16): charge, q_value, score, spectral_angle, CatA_0000_1.mzML, CatA_000...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 12 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): quantCols, group, condition
dbl (1): time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Rows: 2444 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: ","
chr  (6): Protein Accession, Peptide, Used, Candidate, Sample Profile (Ratio...
dbl (25): Protein Group, Protein ID, Quality, Significance, Avg. ppm, Avg. A...
lgl  (1): PTM

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 1 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): tests/testdata/

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Imputing along margin 2 (samples/columns).
Your row data contain missing values. Please read the relevant
section(s) in the aggregateFeatures manual page regarding the effects
of missing values on data aggregation.

Aggregated: 1/1
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 122 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 122 ]
> 
> proc.time()
   user  system elapsed 
459.227   4.890 466.329