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BiocCheckGitClone('MAPFX')
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─ BiocCheckVersion: 1.39.34
─ BiocVersion: 3.19
─ Package: MAPFX
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3349/2445c9c17622723ad32f52590e5e089d5b822a87/MAPFX
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3349/2445c9c17622723ad32f52590e5e089d5b822a87/MAPFX.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAPFX/DESCRIPTION’ ... OK
* this is package ‘MAPFX’ version ‘0.99.3’
* 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 ‘MAPFX’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... 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 ... [20s/20s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'MapfxFFC.Rd':
\examples lines wider than 100 characters:
# create an Output directory in the current working directory for the argument 'Outpath' of the MapfxFFC function
Rd file 'MapfxMPC.Rd':
\examples lines wider than 100 characters:
# create an Output directory in the current working directory for the argument 'Outpath' of the MapfxMPC function
These lines will be truncated in the PDF manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [119s/115s] ERROR
Running examples in ‘MAPFX-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MapfxMPC
> ### Title: MAssively Parallel Flow cytometry Xplorer (MAPFX)
> ### Aliases: MapfxMPC
>
> ### ** Examples
>
> # import built-in data
> data(ord.fcs.raw.meta.df.out_mpc)
> data(ord.fcs.raw.mt_mpc)
>
> # create an Output directory in the current working directory for the argument 'Outpath' of the MapfxMPC function
> dir.create(file.path(tempdir(), "MPC_impu_Output"))
>
> # When `impute = TRUE`, randomly selecting 50% of the cells in each well for model training
> set.seed(123)
> MapfxMPC_impu_obj <- MapfxMPC(
+ runVignette = TRUE, #set FALSE if not running this example
+ runVignette_meta = ord.fcs.raw.meta.df.out_mpc, #set NULL if not running this example
+ runVignette_rawInten = ord.fcs.raw.mt_mpc, #set NULL if not running this example
+ FCSpath = NULL, # users specify their own input path if not running this example
+ Outpath = file.path(tempdir(), "MPC_impu_Output"),
+ file_meta = "auto",
+ bkb.v = c(
+ "FSC-H", "FSC-W", "SSC-H", "SSC-W", "CD69-CD301b", "MHCII",
+ "CD4", "CD44", "CD8", "CD11c", "CD11b", "F480",
+ "Ly6C", "Lineage", "CD45a488", "CD24", "CD103"),
+ yvar = "Legend",
+ control.wells = c(
+ "P1_A01", "P2_A01", "P3_A01",
+ "P3_F04", "P3_F05", "P3_F06", "P3_F07", "P3_F08",
+ "P3_F09", "P3_F10", "P3_F11", "P3_F12",
+ "P3_G01", "P3_G02"),
+ bkb.upper.quantile = 0.9,
+ bkb.lower.quantile = 0.1,
+ bkb.min.quantile = 0.01,
+ inf.lower.quantile = 0.1,
+ inf.min.quantile = 0.01,
+ plots.bkc.bkb = TRUE, plots.bkc.inf = TRUE,
+ plots.initM = TRUE,
+ plots.rmWellEffect = TRUE,
+ impute = TRUE,
+ models.use = c("XGBoost"),
+ extra_args_regression_params = list(list(nrounds = 1500, eta = 0.03)),
+ prediction_events_downsampling = NULL,
+ impu.training = FALSE,
+ plots.imputation = TRUE,
+ cluster.analysis.bkb = TRUE, plots.cluster.analysis.bkb = TRUE,
+ cluster.analysis.all = TRUE, plots.cluster.analysis.all = TRUE,
+ cores = 4L)
Creating directories for output...
Background correcting backbone markers...
Estimating parameters for calibration...
backbone: 1
backbone: 2
backbone: 3
backbone: 4
backbone: 5
backbone: 6
backbone: 7
backbone: 8
backbone: 9
backbone: 10
backbone: 11
backbone: 12
backbone: 13
backbone: 14
backbone: 15
backbone: 16
backbone: 17
Estimation of parameters... Completed!
Calibrating backbone markers (except for physical measurements)...
Calibration of backbone markers... Completed!
Background correcting infinity markers...
Estimating parameters for calibration AND calibrating infinity markers...
Could not find enough cells (>=10) when used "mle.mean+3*mle.sd", so estimated alpha with the top 10 cells with "the largest values":
25 wells applied this strategy
See Wellname_largest10.csv in the intermediary directory for details.
Calibration of infinity markers... Completed!
Forming a matrix of biology (M) for removal of well effect...
Forming logicle functions...
Logicle transforming raw intensity...
Centring logicle transformed intensities...
Centred logicle backbone data... Obtained!
Deriving initial clusters with PhenoGraph (forming the M matrix)...
Run Rphenograph starts:
-Input data of 13300 rows and 17 columns
-k is set to 50
Finding nearest neighbors...
DONE ~4.589s
Compute jaccard coefficient between nearest-neighbor sets...
DONE ~11.839s
Build undirected graph from the weighted links...
DONE ~3.36000000000001s
Run louvain clustering on the graph ...
DONE ~1.972s
Run Rphenograph DONE, totally takes 21.76s.
Return a community class
-Modularity value:0.877501268487132
-Number of clusters:17
23.3955752849579
UMAP with backbones (MPC)/proteins (FFC)...
57.3151955604553
Visualising clusters...
Completed!
Removal of well effect...
Estimating coefficients for removing well effect (Rfast - pre.adj)...
Processing backbone: 1
Processing backbone: 2
Processing backbone: 3
Processing backbone: 4
Processing backbone: 5
Processing backbone: 6
Processing backbone: 7
Processing backbone: 8
Processing backbone: 9
Processing backbone: 10
Processing backbone: 11
Processing backbone: 12
Processing backbone: 13
Processing backbone: 14
Processing backbone: 15
Processing backbone: 16
Processing backbone: 17
Estimation completed!
Removing well effect for backbone markers...
Adjustment completed!
Examining the existence of well effect in the adjusted data (Rfast - post.adj)...
Processing backbone: 1
Processing backbone: 2
Processing backbone: 3
Processing backbone: 4
Processing backbone: 5
Processing backbone: 6
Processing backbone: 7
Processing backbone: 8
Processing backbone: 9
Processing backbone: 10
Processing backbone: 11
Processing backbone: 12
Processing backbone: 13
Processing backbone: 14
Processing backbone: 15
Processing backbone: 16
Processing backbone: 17
Imputation got started...
Fitting regression models...
Error in .check_ncores(length(names)) : 4 simultaneous processes spawned
Calls: MapfxMPC ... imputation_bkb.predictors -> <Anonymous> -> makePSOCKcluster -> .check_ncores
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [118s/115s]
[118s/115s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MAPFX)
>
> test_check("MAPFX")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-MapfxMPC.R:9:1'): (code run outside of `test_that()`) ──────────
Error in `.check_ncores(length(names))`: 4 simultaneous processes spawned
Backtrace:
▆
1. └─MAPFX::MapfxMPC(...) at test-MapfxMPC.R:9:1
2. └─MAPFX:::imputation_bkb.predictors(...)
3. └─parallel::makeCluster(min(cores, length(unique(events.code))))
4. └─parallel::makePSOCKcluster(names = spec, ...)
5. └─parallel:::.check_ncores(length(names))
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
Error: Test failures
Execution halted
* 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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3349/2445c9c17622723ad32f52590e5e089d5b822a87/MAPFX.Rcheck/00check.log’
for details.
===============================
BiocCheck('MAPFX_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.39.34
─ BiocVersion: 3.19
─ Package: MAPFX
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/RtmpWBqqyO/filed4d8e1239e991/MAPFX
─ installDir: /tmp/RtmpWBqqyO/filed4d8e1d22494e
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3349/2445c9c17622723ad32f52590e5e089d5b822a87/MAPFX.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (12%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MAPFX...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 458 lines (15%) are > 80 characters
long.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 3 NOTES
See the MAPFX.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.