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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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mspms.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    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 ‘1.2.0’
* 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 ‘mspms’ 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 ... NOTE
calc_limma_design_matrix: no visible global function definition for
  ‘model.matrix’
limma_stats: no visible binding for global variable ‘peptide’
limma_stats: no visible binding for global variable ‘contrast’
limma_stats: no visible binding for global variable ‘group1’
limma_stats: no visible binding for global variable ‘time’
Undefined global functions or variables:
  contrast group1 model.matrix peptide time
Consider adding
  importFrom("stats", "model.matrix", "time")
to your NAMESPACE file.
* 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    133.232  1.051 207.504
plot_heatmap      23.938  0.701  38.667
limma_stats       10.915  0.433  16.280
prepare_peaks      5.758  0.084   9.036
prepare_fragpipe   4.749  0.104   7.320
plot_pca           3.458  0.067   5.573
* 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-3.22-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/4.5-arm64/Resources/library’
* installing *source* package ‘mspms’ ...
** this is package ‘mspms’ version ‘1.2.0’
** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> # 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.
841 peptides were removed because they had a quality score < 0.3 (34%)
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: 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.
841 peptides were removed because they had a quality score < 0.3 (34%)
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 7 | SKIP 0 | PASS 118 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 118 ]
> 
> proc.time()
   user  system elapsed 
488.643   5.146 800.083