##############################################################################
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###
### 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 version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-13 00:57:12 UTC
* 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 29.527  0.104  29.797
plot_heatmap   7.474  0.148   7.694
* 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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/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 version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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).

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
The following messages occurred during aggregation:

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.

Occurred during the aggregation of set(s): peptides
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).

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
The following messages occurred during aggregation:

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.

Occurred during the aggregation of set(s): peptides
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
Joining with `by = join_by(quantCols)`
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 122 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 122 ]
> 
> proc.time()
   user  system elapsed 
107.427   1.181 109.529