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This page was generated on 2024-12-12 11:40 -0500 (Thu, 12 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4752 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4464 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4415 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4370 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4279 |
| 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 1327/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsCoreUtils 1.19.0 (landing page) RforMassSpectrometry Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the MsCoreUtils package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/MsCoreUtils.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: MsCoreUtils |
| Version: 1.19.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MsCoreUtils.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MsCoreUtils_1.19.0.tar.gz |
| StartedAt: 2024-12-12 03:04:47 -0500 (Thu, 12 Dec 2024) |
| EndedAt: 2024-12-12 03:10:25 -0500 (Thu, 12 Dec 2024) |
| EllapsedTime: 338.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsCoreUtils.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MsCoreUtils.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MsCoreUtils_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MsCoreUtils.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsCoreUtils/DESCRIPTION’ ... OK
* this is package ‘MsCoreUtils’ version ‘1.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘MsCoreUtils’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 loading without being on the library search path ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘MsCoreUtils/libs/MsCoreUtils.so’:
Found non-API call to R: ‘SETLENGTH’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/MsCoreUtils.Rcheck/00check.log’
for details.
MsCoreUtils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MsCoreUtils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘MsCoreUtils’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c between.c -o between.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c closest.c -o closest.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c impNeighbourAvg.c -o impNeighbourAvg.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c join.c -o join.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c localMaxima.c -o localMaxima.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c lowerConvexHull.c -o lowerConvexHull.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c maxi.c -o maxi.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c morphologicalFilters.c -o morphologicalFilters.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c snip.c -o snip.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c sumi.c -o sumi.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c which.c -o which.o gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o MsCoreUtils.so between.o closest.o impNeighbourAvg.o init.o join.o localMaxima.o lowerConvexHull.o maxi.o morphologicalFilters.o snip.o sumi.o which.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-MsCoreUtils/00new/MsCoreUtils/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MsCoreUtils)
MsCoreUtils.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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(se_na2, package = "QFeatures")
> ## dput(assay(se_na2))
> x <- structure(c(0.32325, 0.332, 0.39725, 0.336733, 0.3288, NA, 0.3475,
+ 0.368452, 0.349182, 0.275, 0.2435, 0.268625, 0.262267, 0.3063,
+ 0.2454, 0.271923, 0.2796, 0.304043, 0.2481, NA, NA, 0.268826,
+ 0.3135, 0.281385, 0.2542, 0.2555, 0.269333, 0.272, 0.285667,
+ 0.259333, 0.2565, 0.26, 0.28325, 0.3015, 0.254, 0.268789, 0.242714,
+ 0.243, 0.2855, 0.284091, 0.262182, 0.25075, 0.292, 0.323125,
+ 0.229333, 0.289648, 0.22925, 0.264793, 0.27875, 0.242, 0.2862,
+ 0.321, 0.2892, 0.351333, 0.2754, 0.24, 0.237417, 0.267, 0.270167,
+ 0.296, 0.283667, 0.257, 0.266286, 0.280935, 0.254667, 0.217,
+ 0.303917, 0.252, 0.2315, 0.2614, 0.275071, 0.230273, 0.28, 0.2685,
+ 0.2565, 0.183, 0.264739, 0.291143, 0.253, 0.251444, 0.234429,
+ 0.270571, 0.284125, 0.338, 0.17, 0.266667, 0.315, 0.254667, 0.257,
+ 0.30135, 0.256333, 0.2125, 0.256333, 0.245167, 0.256333, 0.308333,
+ 0.2768, 0.238773, 0.2638, 0.24375, 0.3195, 0.231, 0.280333, 0.303,
+ 0.3185, 0.267, 0.2786, 0.272211, 0.297, 0.226, 0.2445, 0.2506,
+ 0.223, 0.2935, 0.2368, 0.263667, 0.246708, 0.248, NA, 0.271667,
+ 0.2738, 0.27575, 0.2675, 0.186, 0.305833, 0.250333, 0.2576, 0.271,
+ 0.2806, 0.21725, 0.302353, 0.257889, 0.346, 0.262231, 0.2438,
+ 0.32375, 0.2475, 0.257, 0.24, 0.2925, 0.26405, 0.2714, NA, 0.3125,
+ 0.279, 0.2465, 0.3165, NA, 0.364222, 0.335, 0.342667, 0.373857,
+ 0.352414, 0.279, 0.328, 0.383, 0.2815, 0.266333, 0.244222, 0.282,
+ 0.272286, 0.31725, 0.25475, 0.0388, 0.125, 0.069, 0.083, 0.168,
+ 0.113, 0.150333, 0.0753333, 0.0784, 0.1295, 0.064, 0.071, 0.107667,
+ 0.152667, 0.185, 0.119167, 0.0836667, 0.106077, 0.178, 0.11425,
+ 0.100667, 0.149, 0.106, 0.097, 0.1, 0.079, 0.079, 0.111143, 0.101667,
+ 0.09, 0.096, 0.03, 0.095, 0.0805, 0.0923333, 0.07, 0.119, 0.1038,
+ 0.108444, 0.08, 0.066, 0.0922, 0.119667, 0.119, 0.10025, 0.0986667,
+ 0.06075, 0.0745, 0.0882857, 0.1128, 0.084, 0.100929, 0.0695,
+ 0.0972, 0.12075, 0.153, 0.086, 0.0961667, 0.0825, 0.0915, 0.0978333,
+ 0.129, 0.0870833, 0.0806667, 0.054, 0.07975, 0.085, 0.0703333,
+ 0.1185, 0.163, 0.1134, 0.09875, 0.1775, 0.1455, 0.115667, 0.133,
+ NA, 0.0458333, 0.0881429, 0.116333, 0.0903333, 0.0966667, 0.0494,
+ 0.0671429, 0.07075, 0.0935455, 0.0942979, 0.047, 0.108864, 0.0794,
+ 0.102304, 0.0574286, 0.1099, NA, 0.0935, 0.0931163, 0.104513,
+ 0.081375, 0.072, 0.0756667, 0.09, 0.0463333, 0.1025, 0.0875,
+ 0.073, 0.0813333, 0.09925, 0.099, 0.09764, 0.0481818, 0.0918333,
+ NA, 0.121333, 0.0716471, 0.0528333, 0.0615, 0.079, 0.119333,
+ 0.12425, 0.056, 0.0435, 0.0556667, 0.109, 0.0531429, 0.065, 0.0804444,
+ 0.076, 0.0703333, 0.043, 0.078, 0.0839167, 0.0828182, 0.0945,
+ 0.0916667, 0.06, NA, 0.122375, 0.0658889, 0.06075, 0.0675, 0.0642222,
+ 0.07325, 0.09075, 0.0654444, 0.103, 0.047, 0.108, 0.0385, 0.0834286,
+ 0.095, 0.0636842, 0.0768333, 0.0876667, NA, 0.0684286, 0.0905714,
+ 0.179, 0.046, 0.079, 0.0555, NA, 0.079, 0.076, 0.086, 0.07675,
+ 0.0325, 0.083, 0.0668, 0.0764, 0.08525, 0.1178, 0.09275, 0.0705,
+ 0.0791111, 0.11, 0.0765, 0.1242, 0.161, 0.1059, 0.1625, 0.1,
+ 0.134, 0.113, 0.14, 0.127, 0.130667, 0.081, 0.1314, 0.0925, 0.114667,
+ 0.0662, 0.1285, 0.144714, 0.282, 0.2214, 0.2, 0.2375, 0.159667,
+ 0.211923, NA, 0.2185, 0.172333, 0.1975, 0.160667, 0.167, 0.116,
+ 0.16675, 0.187, 0.1645, 0.070625, 0.095, 0.0913333, 0.1715, 0.0945714,
+ 0.31875, 0.2852, 0.35375, 0.3852, NA, 0.2965, 0.275167, 0.314,
+ 0.3035, 0.2548, NA, 0.291, 0.320083, 0.3105, 0.345667, 0.2462,
+ 0.305667, 0.2722, 0.289, 0.29475, 0.332571, 0.272, 0.273, 0.274,
+ 0.234667, 0.240333, 0.2175, 0.324, 0.46, 0.46075, 0.471, 0.402667,
+ 0.4135, 0.0423333, 0.059, 0.0854444, 0.0723333, 0.047125, 0.0435,
+ 0.08825, 0.0754, 0.104, 0.193, 0.0736, 0.0498, 0.0701667, 0.0775,
+ 0.155571, 0.1592, 0.214333, 0.165, 0.1763, 0.163667, 0.169222,
+ 0.1565, 0.168333, 0.19, 0.173, 0.178, 0.1515, 0.1685, 0.199,
+ NA, 0.160167, 0.1874, 0.16225, 0.173857, 0.223, 0.166737, 0.222,
+ 0.179533, 0.179, 0.174333, 0.1995, 0.197333, NA, 0.1892, 0.167,
+ NA, 0.207, 0.182, 0.18875, 0.181727, 0.17, 0.181, 0.17, 0.1795,
+ 0.1605, 0.172, 0.167111, 0.154, 0.1645, 0.163167, 0.163, 0.169,
+ 0.182, NA, 0.239, 0.1905, 0.232, 0.177667, 0.174417, 0.185, 0.218125,
+ 0.159333, 0.178, NA, 0.168, 0.023, 0.1194, 0.16525, 0.1574, 0.166,
+ 0.155667, NA, 0.1446, 0.154, 0.161, 0.0438, 0.049, 0.0695, 0.096,
+ 0.014, 0.0495, NA, 0.341, 0.361125, 0.307167, 0.3365, 0.307,
+ 0.24625, 0.193, 0.314, 0.3354, 0.264, 0.198, 0.2645, 0.18075,
+ NA, 0.191, 0.235, 0.2175, 0.0896, 0.2715, 0.061, 0.246, 0.235,
+ 0.268, 0.233, 0.3695, 0.36125, 0.343, 0.32075, 0.366333, 0.1934,
+ 0.206444, 0.13, 0.21375, 0.1658, 0.2605, 0.062, 0.1945, 0.175,
+ 0.06825, NA, 0.1855, 0.2535, 0.291, 0.1355, 0.413, 0.164, 0.141667,
+ 0.155667, 0.275, 0.13775, NA, 0.0573333, 0.156, 0.1365, 0.282,
+ 0.3145, 0.24375, 0.252333, 0.131, 0.176636, 0.275667, 0.26925,
+ 0.243, 0.0862, 0.112, 0.209833, 0.183, 0.4195, 0.144, 0.2485,
+ NA, 0.2094, 0.254, 0.247667, 0.237, 0.136875, 0.2082, NA, NA,
+ 0.390333, 0.381, 0.081, 0.145, 0.2175, 0.292, 0.241, 0.1516,
+ 0.386882, 0.0734, 0.304667, 0.14, NA, 0.13, 0.1478, 0.1898, 0.4055,
+ 0.291333, 0.1782, 0.471, 0.205, 0.165, 0.148286, 0.248, 0.181,
+ 0.257333, 0.156333, 0.238, 0.203, 0.114, 0.326, 0.2245, 0.2755,
+ 0.2914, 0.250333, 0.144, 0.316667, 0.254, 0.259667, 0.287, 0.1818,
+ 0.1185, 0.21, 0.269571, 0.214333, 0.244818, 0.23, 0.1882, 0.125,
+ 0.228, 0.0766667, 0.125333, 0.076, 0.248, 0.217, 0.02, 0.236,
+ 0.281, 0.238, 0.1225, 0.1655, 0.16, 0.0618571, NA, 0.127, 0.17,
+ 0.195, 0.201, 0.0688333, 0.2135, 0.229, 0.187655, 0.1916, 0.196,
+ 0.295, 0.181, 0.136, 0.1525, 0.225, 0.248, 0.167, 0.086, NA,
+ 0.18025, 0.244, 0.259, 0.14825, 0.2445, NA, 0.56, 0.504167, 0.499,
+ 0.588, 0.5515, 0.5015, 0.4515, 0.5595, 0.507318, 0.527625, NA,
+ 0.591, 0.512714, 0.498, 0.4835, 0.4925, NA, 0.497, 0.4318, 0.2755,
+ 0.279667, 0.2465, NA, NA, NA, 0.2545, 0.290032, 0.288273, 0.276,
+ 0.3015, 0.311625, 0.302, 0.3127, 0.3168, 0.278808, 0.3089, 0.318,
+ 0.316, 0.297667, 0.295, 0.309978, 0.316, 0.324077, 0.2974, 0.319,
+ 0.285333, 0.3032, 0.309, 0.295, 0.303667, 0.312, 0.32575, 0.315,
+ 0.3025, 0.318044, 0.306143, 0.242, 0.2885, 0.321333, 0.327091,
+ 0.3575, 0.281, 0.32425, NA, 0.308815, 0.33475, 0.289276, 0.34725,
+ 0.301, 0.328933, NA, 0.3222, 0.301333, 0.332, 0.296667, 0.310417,
+ 0.335, 0.346833, 0.316538, 0.322, 0.241, 0.278429, 0.314742,
+ 0.327667, 0.2935, 0.322083, 0.283, 0.2915, NA, 0.308143, 0.299614,
+ 0.313667, 0.334, 0.28925, 0.335, 0.299978, 0.306714, NA, 0.323,
+ 0.365571, 0.282, 0.3295, 0.344, 0.292, 0.316333, NA, 0.318667,
+ 0.3125, 0.31275, 0.310333, 0.268, 0.316, 0.283, 0.301667, 0.307333,
+ 0.2934, 0.311273, 0.2828, 0.2775, 0.307, 0.354, 0.314833, 0.2965,
+ 0.283, 0.334, 0.305, 0.301526, 0.30825, 0.271, 0.3015, 0.3439,
+ 0.304, 0.31, 0.2903, 0.298333, 0.328917, 0.314, 0.293, 0.323,
+ 0.2878, 0.306, 0.299833, 0.326, 0.308, 0.355667, 0.3254, 0.321,
+ 0.3024, NA, 0.312353, 0.311667, 0.306, 0.316, 0.2908, NA, 0.306909,
+ 0.286, 0.3218, 0.30075, 0.2886, 0.3086, 0.295714, 0.305, 0.3245,
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+ c("M1F1A", "M1F4A", "M1F7A", "M1F11A", "M1F2B",
+ "M1F5B", "M1F8B", "M1F11B", "M2F1A", "M2F4A", "M2F7A", "M2F11A",
+ "M2F2B", "M2F5B", "M2F8B", "M2F11B")))
>
> ## dput(rowData(se_na2)$randna)
> randna <- c(TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, FALSE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
+ TRUE, TRUE, TRUE)
>
> library("testthat")
> library("MsCoreUtils")
Attaching package: 'MsCoreUtils'
The following object is masked from 'package:stats':
smooth
>
> test_check("MsCoreUtils")
Iterations of EM:
1...2...
[1] 0.07947339
Iterations of EM:
1...2...3...4...5...6...7...8...9...10...11...12...13...14...
[1] 0.990058
Iterations of EM:
1...2...3...4...5...6...7...8...9...10...11...12...13...14...
[1] 0.990058
[1] 1.290994
[1] 5.163978
Iterations of EM:
1...2...3...4...5...6...7...8...
Iterations of EM:
1...2...3...4...5...6...7...8...
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 603 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 603 ]
>
> proc.time()
user system elapsed
67.027 0.405 67.427
MsCoreUtils.Rcheck/MsCoreUtils-Ex.timings
| name | user | system | elapsed | |
| aggregate | 0.753 | 0.061 | 0.815 | |
| binning | 0.002 | 0.000 | 0.001 | |
| breaks_ppm | 0.001 | 0.000 | 0.001 | |
| check | 0.000 | 0.000 | 0.001 | |
| coerce | 0 | 0 | 0 | |
| colCounts | 0.001 | 0.000 | 0.000 | |
| common_path | 0.000 | 0.000 | 0.001 | |
| distance | 0.001 | 0.000 | 0.001 | |
| entropy | 0.000 | 0.000 | 0.001 | |
| estimateBaseline | 0.052 | 0.002 | 0.054 | |
| force_sorted | 0.001 | 0.000 | 0.001 | |
| formatRt | 0.001 | 0.000 | 0.001 | |
| gnps | 0.005 | 0.000 | 0.004 | |
| group | 0.001 | 0.000 | 0.001 | |
| i2index | 0.001 | 0.000 | 0.000 | |
| imputation | 0.009 | 0.001 | 0.010 | |
| localMaxima | 0.000 | 0.000 | 0.001 | |
| matching | 0.001 | 0.002 | 0.002 | |
| maxi | 0.000 | 0.000 | 0.001 | |
| medianPolish | 0.000 | 0.001 | 0.002 | |
| noise | 0.000 | 0.000 | 0.001 | |
| normalize | 0.004 | 0.002 | 0.006 | |
| peakRegionMask | 0.000 | 0.000 | 0.001 | |
| ppm | 0 | 0 | 0 | |
| range | 0 | 0 | 0 | |
| rbindFill | 0.004 | 0.001 | 0.006 | |
| refineCentroids | 0.054 | 0.000 | 0.054 | |
| rla | 0.000 | 0.001 | 0.002 | |
| robustSummary | 0.004 | 0.001 | 0.005 | |
| smooth | 0.009 | 0.000 | 0.009 | |
| sumi | 0.000 | 0.000 | 0.001 | |
| validation | 0.000 | 0.001 | 0.001 | |
| valleys | 0.001 | 0.001 | 0.002 | |
| vapply | 0 | 0 | 0 | |
| which | 0.000 | 0.000 | 0.001 | |