Nils Kurzawa
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/NPARC |
| git_branch: RELEASE_3_17 |
| git_last_commit: 2bd229b |
| git_last_commit_date: 2023-04-25 11:14:31 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1395/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NPARC 1.12.0 (landing page) Nils Kurzawa
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the NPARC package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: NPARC |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NPARC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NPARC_1.12.0.tar.gz |
| StartedAt: 2023-10-18 11:51:58 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 11:53:38 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 100.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NPARC.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NPARC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NPARC_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/NPARC.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NPARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NPARC’ version ‘1.12.0’
* 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 ‘NPARC’ 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 R 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 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
getParams 8.229 0.117 12.354
NPARCtest 3.547 0.077 5.326
runNPARC 3.392 0.056 5.270
nparcFit 3.361 0.055 5.239
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘init_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
NPARC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NPARC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘NPARC’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** 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 (NPARC)
NPARC.Rcheck/tests/init_tests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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.
> data(stauro_TPP_data_tidy)
Warning message:
In data(stauro_TPP_data_tidy) : data set 'stauro_TPP_data_tidy' not found
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(magrittr)
> library(NPARC)
> library(testthat)
Attaching package: 'testthat'
The following objects are masked from 'package:magrittr':
equals, is_less_than, not
The following object is masked from 'package:dplyr':
matches
>
> ATP_targets_stauro <- filter(stauro_TPP_data_tidy, grepl("ATP|STK4_", uniqueID))
> atp_ids <- ATP_targets_stauro$uniqueID
> rss0_ref <- c( 0.042328688, 0.574210782, 1.105606894, 66.141814549, 1.279980245, 1.445979905, NA, 0.085035397, NA, 0.086908456, 0.040746912, 0.229219646, 0.185040763, 0.069901302, 3.219166488, 0.890621716, 1.482869417, 0.111385691, 0.890474276, 0.096161260, 0.005317976, 0.165361410, 0.261380998, 2.004720774, NA, 1.017639038, 0.037805608, 0.079748130, 0.080865091, 0.023917017, 0.302070404, 0.438928745, 0.021234921, 0.207783991, 0.511561035, NA, 0.047061699, 0.022204837, 0.018557014, 82.669418181, 0.171696257, 0.246755638, 0.027504901, 0.042566445, 0.685432518, 1.2181315672231198821)
> rss1_ref <- c( NA, 0.52452012, 1.02728630, NA, 1.16253040, NA, NA, NA, NA, 0.08085710, 0.03391284, 0.19178616, 0.11715310, 0.05738689, 2.85347619, NA, 0.88566800, NA, 0.86233078, 0.05913776, NA, NA, 0.24112396, NA, NA, NA, 0.03726856, 0.07672426, 0.07933303, 0.02046256, NA, 0.42376129, 0.01929703, 0.19330061, 0.49355960, NA, 0.03926680, 0.01932926, NA, 82.39894648, 0.14698662, 0.22814391, 0.02189395, 0.03691358, 0.57373856, 0.083147452021042442)
> rssDiff_ref <- c(NA, 0.0496906604, 0.0783205890, NA, 0.1174498426, NA, NA, NA, NA, 0.0060513570, 0.0068340678, 0.0374334892, 0.0678876612, 0.0125144109, 0.3656902966, NA, 0.5972014163, NA, 0.0281434961, 0.0370234978, NA, NA, 0.0202570335, NA, NA, NA, 0.0005370464, 0.0030238719, 0.0015320641, 0.0034544609, NA, 0.0151674541, 0.0019378859, 0.0144833862, 0.0180014361, NA, 0.0077948980, 0.0028755747, NA, 0.2704717055, 0.0247096421, 0.0186117273, 0.0056109477, 0.0056528626, 0.1116939612, 1.13498411520207742598)
> n0_ref <- c(10, 40, 40, 20, 20, 20, 0, 20, 0, 40, 40, 40, 40, 40, 20, 10, 20, 10, 40, 30, 10, 10, 20, 20, 0, 10, 30, 40, 40, 40, 10, 40, 40, 30, 40, 0, 40, 30, 10, 20, 40, 40, 40, 40, 40, 40)
> n1_ref <- c(10, 40, 40, 20, 20, 20, 0, 20, 0, 40, 40, 40, 40, 40, 20, 10, 20, 10, 40, 30, 10, 10, 20, 20, 0, 10, 30, 40, 40, 40, 10, 40, 40, 30, 40, 0, 40, 30, 10, 20, 40, 40, 40, 40, 40, 40)
> repeats_ref <- c(11, 0, 0, 11, 0, 11, 11, 11, 11, 0, 0, 0, 0, 0, 0, 11, 0, 11, 0, 0, 11, 11, 0, 11, 11, 11, 0, 0, 0, 0, 11, 0, 0, 0, 0, 11, 0, 0, 11, 0, 0, 0, 0, 0, 0, 0)
> tm_0_ref <- c(NA, 61.733018503993208, NaN, NA, NaN, NaN, NA, NA, NA, 45.507090381927227, 48.370656179268586, 46.177862386428778, NaN, 50.747974622093842, 51.108100718477552, NA, 53.716668890572350, NA, 49.944382649054042, 53.268268043773986, NA, 64.083619744519751, 52.630782071773126, 54.403632566800773, NA, NA, 49.973318102061327, 54.987190448048963, 55.650774547079479, 53.776217585739715, NA, 63.931766238670086, 53.474065831051554, 59.660513721432004, 53.651458551339147, NA, 53.400317830126923, 56.166341210006678, NA, 49.957133804531374, 58.379308939431617, 61.739135919243360, 49.739613672120782, 51.424194381078600, NaN, 51.075584610286953)
> tm_20_ref <- c(51.826211134785211, 66.548397028205514, 77.195149424582979, 55.304171825879109, 54.826147979730159, NA, NA, 56.362667583506500, NA, 45.626792065465864, 48.448244898573385, 47.460807063834899, 60.921156578436033, 50.709466817179830, NaN, NaN, NaN, 53.705720351822045, 50.199251315345073, 51.808623346193485, 54.052321351744041, NA, 51.186531862923864, NA, NA, NaN, 50.030558335114812, 54.702758421926561, 55.813688161147894, 53.533856781624372, 49.760889873698368, 63.528237092905130, 53.782382421569636, 60.003138034648828, 53.162997375385423, NA, 53.292278053288818, 56.235749170195618, 53.673086380853192, 55.280037025265500, 59.676701562973001, 60.694252715919731, 49.732243787451694, 51.158615360263845, 70.641541915911802, 59.740907732406420)
> pAdj_ref <- c(NA, 0.699795397624508708, 0.753523752550566694, NA, 0.861339846144721699, NA, NA, NA, NA, 0.753523752550566694, 0.315762492309564990, 0.315762492309564990, 0.019064553849503785, 0.315762492309564990, 0.861339846144721699, NA, 0.315762492309564990, NA, 0.861339846144721699, 0.077448008418172787, NA, NA, 0.861339846144721699, NA, NA, NA, 0.983055252694920556, 0.861339846144721699, 0.945666731555014795, 0.368321920466761210, NA, 0.861339846144721699, 0.695132899776564450, 0.861339846144721699, 0.861339846144721699, NA, 0.315762492309564990, 0.695132899776564450, NA, 0.997288089402401878, 0.368321920466761210, 0.753523752550566694, 0.315762492309564990, 0.411224424237822794, 0.315762492309564990, 0.000000000000000000)
>
>
> proc.time()
user system elapsed
1.562 0.168 2.640
NPARC.Rcheck/NPARC-Ex.timings
| name | user | system | elapsed | |
| NPARCtest | 3.547 | 0.077 | 5.326 | |
| fitSingleSigmoid | 0.410 | 0.012 | 0.540 | |
| getParams | 8.229 | 0.117 | 12.354 | |
| nparcFit | 3.361 | 0.055 | 5.239 | |
| runNPARC | 3.392 | 0.056 | 5.270 | |