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This page was generated on 2024-12-22 09:21 -0500 (Sun, 22 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-12-18 r87448) -- "Unsuffered Consequences" | 852 |
| 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 140/216 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| MsCoreUtils 1.19.0 (landing page) RforMassSpectrometry Package Maintainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
|
To the developers/maintainers of the MsCoreUtils 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: MsCoreUtils |
| Version: 1.19.0 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MsCoreUtils.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MsCoreUtils_1.19.0.tar.gz |
| StartedAt: 2024-12-22 08:29:02 -0500 (Sun, 22 Dec 2024) |
| EndedAt: 2024-12-22 08:30:33 -0500 (Sun, 22 Dec 2024) |
| EllapsedTime: 90.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsCoreUtils.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MsCoreUtils.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MsCoreUtils_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsCoreUtils.Rcheck’
* using R Under development (unstable) (2024-12-18 r87448)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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 ... 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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
‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsCoreUtils.Rcheck/00check.log’
for details.
MsCoreUtils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL MsCoreUtils ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘MsCoreUtils’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c between.c -o between.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c closest.c -o closest.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c impNeighbourAvg.c -o impNeighbourAvg.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init.c -o init.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c join.c -o join.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c localMaxima.c -o localMaxima.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c lowerConvexHull.c -o lowerConvexHull.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c maxi.c -o maxi.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c morphologicalFilters.c -o morphologicalFilters.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c snip.c -o snip.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c sumi.c -o sumi.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c which.c -o which.o gcc -shared -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 installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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) (2024-12-18 r87448) -- "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,
+ 0.3245, 0.315, 0.31, 0.265222, 0.278, NA, 0.270429, 0.295776,
+ 0.294, 0.25, 0.261, 0.29625, 0.296, 0.271611, 0.277667, 0.282857,
+ 0.29375, 0.30025, 0.2522, 0.227, 0.2085, 0.2, 0.2165, 0.2075,
+ 0.257167, 0.230333, 0.3088, 0.213, 0.2045, 0.1725, 0.278333,
+ 0.218333, 0.198, 0.178333, 0.196333, 0.206231, 0.272, 0.19725,
+ 0.234667, 0.278, 0.186, 0.179, 0.259, NA, 0.1736, 0.214, 0.209667,
+ 0.2165, 0.1752, 0.323, 0.282895, 0.3125, 0.28, 0.187364, 0.2684,
+ NA, 0.281778, 0.244, 0.2655, 0.1672, 0.275, 0.209, 0.28125, 0.308667,
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+ 0.271571, 0.282, 0.235, 0.277, NA, 0.2572, 0.291286, 0.2676,
+ 0.2705, 0.27325, 0.312, 0.280857, 0.2725, 0.235619, 0.254429,
+ 0.255833, 0.290333, NA, 0.247333, 0.235, 0.249, 0.1955, 0.275,
+ 0.2675, 0.2995, 0.245667, 0.295, 0.254143, 0.2575, 0.2456, NA,
+ 0.2865, 0.2655, 0.278556, 0.298333, 0.25125, 0.2328, 0.337167,
+ 0.269778, 0.235333, 0.28125, 0.2455, 0.243, 0.262318, NA, 0.2635,
+ 0.262, 0.26325, NA, 0.28475, 0.209, 0.256111, 0.3072, 0.275,
+ NA, NA, 0.248111, 0.4205, 0.437333, 0.458167, 0.4435, 0.4178,
+ 0.4335, 0.436667, 0.385167, 0.486667, 0.45856, 0.459455, 0.446667,
+ 0.4335, 0.465048, 0.450737, 0.466667, 0.477, 0.446, 0.472, 0.468,
+ 0.469833, 0.445571, 0.468929, 0.4585, NA, 0.500667, 0.528, 0.5235,
+ 0.541, 0.557, 0.542, 0.4425, 0.53375, 0.470333, 0.595, 0.575,
+ 0.548333, 0.573286, 0.464857, 0.4118, 0.412667, 0.46, 0.4275,
+ 0.401375, 0.467833, 0.4525, 0.4582, 0.4686, 0.4235, NA, 0.461,
+ 0.492, 0.432, 0.386, 0.433176, 0.434, 0.474667, 0.426375, 0.434333,
+ 0.454778, 0.449833, 0.493, 0.483, 0.428286, 0.458125, 0.4812,
+ 0.432, 0.4675, 0.386, 0.4445, 0.504, 0.423667, 0.4035, 0.462,
+ 0.451231, 0.484667, 0.44, 0.429, 0.466, NA, 0.558667, 0.6245,
+ NA, 0.531333, 0.534, NA, 0.508, 0.44975, 0.50875, 0.487667, 0.511571,
+ 0.558, 0.55775, 0.5495, 0.5295, 0.565333, 0.536, 0.530286, 0.5355,
+ 0.6435, 0.3835, 0.45, 0.440167, 0.455, 0.468286, 0.389, 0.448333,
+ 0.466, 0.432, 0.4848, 0.382, 0.3944, 0.4525, 0.483429, 0.4605,
+ 0.4615, 0.437143, 0.166667, 0.25575, NA, 0.222222, 0.190667,
+ 0.17455, 0.1925, 0.16725, 0.221333, 0.211, 0.244, 0.216, 0.1883,
+ 0.2099, 0.227, 0.209, NA, 0.2515, 0.194667, 0.2545, 0.2162, 0.148,
+ 0.14425, 0.14, 0.157889, 0.1262, 0.162579, 0.27775, 0.287, 0.267,
+ 0.298, 0.265, NA, 0.188444, 0.263333, 0.278, 0.3135, 0.276667,
+ 0.335333, 0.27575, 0.295, 0.366667, 0.479, 0.479, 0.4382, 0.403,
+ 0.499, 0.509556, 0.179667, 0.2232, 0.19075, 0.1905, NA, 0.21,
+ 0.51, 0.557, 0.46, 0.435, 0.515333, 0.50225, NA, 0.483, 0.446,
+ 0.516, 0.395, 0.37, 0.396, 0.466, 0.3415, 0.342375, 0.3495, 0.321,
+ 0.3486, 0.268, 0.344, 0.316278, 0.3505, 0.369, 0.3192, 0.3595,
+ NA, 0.3196, 0.32475, 0.344, 0.341125, 0.3684, 0.309125, 0.328143,
+ NA, 0.363, 0.308, 0.359182, 0.375333, 0.36, 0.3304, 0.386, 0.324111,
+ 0.34225, 0.3865, 0.351375, 0.268, 0.315, 0.3507, 0.318667, 0.379,
+ 0.329333, 0.341, 0.3525, 0.277, 0.325, 0.343929, 0.336333, 0.337222,
+ 0.342375, 0.325222, 0.35325, 0.317429, 0.311667, 0.2758, 0.3336,
+ 0.32, 0.3055, 0.335643, 0.295667, NA, 0.352, 0.3075, 0.307, NA,
+ 0.4579, 0.30225, 0.2696, 0.329833, NA, 0.331, 0.255667, 0.3165,
+ 0.3285, 0.3106, 0.464625, 0.480667, 0.487571, 0.4888, 0.5465,
+ 0.52625, 0.137, 0.2175, 0.287667, 0.27025, 0.285, NA, 0.201,
+ 0.3255, 0.288, 0.213667, 0.3686, 0.303, NA, 0.305, 0.283, 0.3275,
+ 0.278, 0.302, 0.383, 0.189, 0.251, 0.32, 0.306, 0.3218, 0.293167,
+ 0.2865, 0.309667, 0.263, 0.383333, NA, 0.350667, 0.237333, NA,
+ NA, 0.2858, 0.255667, 0.300667, 0.2775, 0.323, 0.2896, 0.297625,
+ 0.267, 0.2845, 0.278, NA, 0.23625, 0.2687, 0.28875, 0.3336, 0.309417,
+ 0.4224, 0.2614, 0.504, 0.286333, 0.320667, 0.288, 0.18825, 0.324667,
+ 0.1555, 0.3105, 0.276667, 0.2765, 0.232333, 0.2835, NA, 0.296,
+ NA, 0.191, 0.19575, 0.372, 0.259, 0.2815, 0.197, 0.32575, 0.187333,
+ 0.188, 0.293, 0.23, 0.2125, 0.3192, 0.2, NA, 0.393, 0.417, 0.243667,
+ NA, 0.302, 0.304188, 0.191091, 0.412, 0.194333, 0.333, 0.367,
+ 0.374667, 0.373667, 0.3655, 0.248, 0.30925, 0.26725, 0.241, 0.4835,
+ 0.303667, 0.357, 0.2295, 0.2902, 0.244375, 0.36, 0.19425, 0.19,
+ 0.3672, NA, 0.279, 0.1435, 0.28875, 0.311, 0.3055, 0.30025, 0.2925,
+ 0.253, 0.256, 0.285, 0.2565, 0.222667, 0.147444, 0.296333, 0.437,
+ 0.1985, 0.185, 0.29125, NA, 0.252, 0.38725, 0.239, 0.2966, 0.1885,
+ 0.232, 0.478, 0.314, 0.3475, 0.304, 0.224286, 0.331, 0.348, 0.269083,
+ 0.477, 0.2565, NA, 0.165778, 0.2386, 0.412, 0.294, 0.243219,
+ 0.3011, 0.2652, 0.264, 0.2935, 0.2635, NA, 0.215, NA, 0.315,
+ 0.42, NA, 0.240167, 0.214333, 0.313, 0.372, 0.2975, 0.222, NA,
+ NA, 0.22, 0.184, 0.180667, 0.144, 0.212222, 0.168333, 0.201333,
+ NA, 0.1685, 0.2025, 0.214, 0.197667, 0.152167, 0.154833, 0.160333,
+ 0.1552, 0.2074),
+ .Dim = c(689L, 16L),
+ .Dimnames = list(c("AT1G09210",
+ "AT1G21750", "AT1G51760", "AT1G56340", "AT2G32920", "AT2G47470",
+ "AT3G54960", "AT4G24190", "AT5G60640", "AT1G07810", "AT1G32210",
+ "AT1G34130", "AT1G54990", "AT1G61790", "AT1G67490", "AT1G67730",
+ "AT1G76400", "AT2G01470", "AT2G01720", "AT2G03120", "AT2G16530",
+ "AT2G21160", "AT2G38960", "AT2G39960", "AT2G45140", "AT2G46170",
+ "AT3G05230", "AT3G07140", "AT3G07180", "AT3G52190", "AT3G55360",
+ "AT3G57220", "AT3G57650", "AT4G01320", "AT4G09580", "AT4G21150",
+ "AT4G32130", "AT4G36480", "AT4G37640", "AT5G07340", "AT5G19690",
+ "AT5G45160", "AT5G48810", "AT5G53560", "AT5G55940", "AT5G61790",
+ "AT5G62390", "AT5G66680", "AT1G02120", "AT1G08470", "AT1G11680",
+ "AT1G14010", "AT1G18260", "AT1G18540", "AT1G18700", "AT1G19370",
+ "AT1G20330", "AT1G22200", "AT1G27770", "AT1G35620", "AT1G51570",
+ "AT1G52260", "AT1G52600", "AT1G55850", "AT1G61770", "AT1G63050",
+ "AT1G64090", "AT1G64950", "AT1G65020", "AT1G65270", "AT1G65820",
+ "AT1G70770", "AT1G71780", "AT1G75140", "AT1G79940", "AT2G01250",
+ "AT2G03510", "AT2G04350", "AT2G16760", "AT2G20990", "AT2G21600",
+ "AT2G24180", "AT2G24420", "AT2G25110", "AT2G33630", "AT2G45510",
+ "AT3G01380", "AT3G03330", "AT3G13410", "AT3G13870", "AT3G14610",
+ "AT3G15710", "AT3G18370", "AT3G23190", "AT3G26830", "AT3G28580",
+ "AT3G28720", "AT3G44330", "AT3G48890", "AT3G51430", "AT3G51440",
+ "AT3G51460", "AT3G57010", "AT3G57030", "AT3G57880", "AT3G59500",
+ "AT3G60600", "AT3G62360", "AT3G66658", "AT4G00175", "AT4G11800",
+ "AT4G14420", "AT4G14950", "AT4G15760", "AT4G16170", "AT4G21180",
+ "AT4G24330", "AT4G27090", "AT4G28570", "AT4G29520", "AT4G30210",
+ "AT4G30600", "AT4G31340", "AT4G36220", "AT4G36250", "AT4G37330",
+ "AT4G37370", "AT4G37430", "AT5G03160", "AT5G05670", "AT5G11560",
+ "AT5G13640", "AT5G17980", "AT5G19130", "AT5G20655", "AT5G23575",
+ "AT5G23630", "AT5G24810", "AT5G25900", "AT5G42020", "AT5G42570",
+ "AT5G44920", "AT5G45420", "AT5G47420", "AT5G49945", "AT5G52240",
+ "AT5G52420", "AT5G58640", "AT4G38215", "AT5G57655", "AT1G71220",
+ "AT1G77510", "AT2G30490", "AT2G39630", "AT3G16110", "AT3G24160",
+ "AT3G51050", "AT4G33360", "AT5G17770", "AT5G20520", "AT5G63840",
+ "AT1G44170", "AT3G27325", "AT1G08660", "AT1G19710", "AT1G21480",
+ "AT1G49710", "AT1G51590", "AT1G74380", "AT1G78920", "AT2G20370",
+ "AT2G22900", "AT2G38650", "AT2G47650", "AT3G02350", "AT3G03050",
+ "AT3G07330", "AT3G21160", "AT3G25140", "AT3G48820", "AT3G53520",
+ "AT3G55830", "AT3G61130", "AT4G15240", "AT4G37690", "AT4G38240",
+ "AT4G38270", "AT5G16910", "AT5G18485", "AT5G61840", "AT1G04430",
+ "AT1G04910", "AT1G06890", "AT1G19360", "AT1G19430", "AT1G26850",
+ "AT1G27930", "AT1G29470", "AT1G29790", "AT1G31850", "AT1G51540",
+ "AT1G51630", "AT1G55130", "AT1G72480", "AT1G78240", "AT2G01270",
+ "AT2G01970", "AT2G35610", "AT2G40280", "AT3G13772", "AT3G16200",
+ "AT3G21190", "AT3G23300", "AT3G26370", "AT3G27220", "AT3G27230",
+ "AT3G28480", "AT3G49720", "AT3G56750", "AT3G66654", "AT4G00740",
+ "AT4G00750", "AT4G14360", "AT4G16120", "AT4G17430", "AT4G18030",
+ "AT4G38500", "AT4G39840", "AT5G04060", "AT5G05170", "AT5G11730",
+ "AT5G14430", "AT5G20350", "AT5G35160", "AT5G37310", "AT5G43100",
+ "AT5G44790", "AT5G61240", "AT2G28520", "AT1G03860", "AT1G27390",
+ "AT1G47260", "AT2G19080", "AT2G20800", "AT2G21870", "AT2G29080",
+ "AT2G33040", "AT2G33220", "AT3G01280", "AT3G08580", "AT3G08950",
+ "AT3G20000", "AT3G52300", "AT3G54110", "AT4G01100", "AT4G28510",
+ "AT5G08040", "AT5G09420", "AT5G14040", "AT5G15090", "AT5G19760",
+ "AT5G67500", "NAD5", "ORFB", "AT1G15500", "AT1G79560", "AT1G80300",
+ "AT2G16640", "AT2G47840", "AT3G08640", "AT3G23710", "AT3G46740",
+ "AT4G02510", "AT4G32400", "AT4G33350", "AT5G05000", "RPS7-01",
+ "AT1G06530", "AT1G08480", "AT1G53760", "AT1G65540", "AT2G16460",
+ "AT2G18330", "AT2G20940", "AT2G27730", "AT2G29990", "AT2G42210",
+ "AT2G45060", "AT3G02090", "AT3G16480", "AT3G51010", "AT3G58840",
+ "AT3G59280", "AT3G59820", "AT4G05020", "AT4G26410", "AT4G27585",
+ "AT4G28220", "AT4G28390", "AT4G29130", "AT4G29480", "AT4G30010",
+ "AT4G32470", "AT4G39690", "AT5G05520", "AT5G12290", "AT5G13490",
+ "AT5G13610", "AT5G16930", "AT5G18800", "AT5G20090", "AT5G23300",
+ "AT5G26030", "AT5G27540", "AT5G43970", "AT5G54100", "AT5G55070",
+ "AT5G58270", "AT1G06940", "AT1G11320", "AT1G42960", "AT2G37400",
+ "AT2G37860", "AT2G44640", "AT3G06960", "AT3G45890", "AT3G63170",
+ "AT4G32250", "AT4G39460", "AT5G01500", "AT5G01590", "AT5G08545",
+ "AT5G12470", "AT5G12860", "AT5G19620", "AT5G22790", "AT5G23890",
+ "AT5G24690", "AT5G65250", "AT1G10510", "AT1G50460", "AT1G51980",
+ "AT1G53000", "AT1G77590", "AT2G04940", "AT2G19860", "AT2G26140",
+ "AT2G35720", "AT3G47930", "AT3G56430", "AT5G13450", "AT5G57490",
+ "AT5G63400", "COB", "COX2", "ORF25", "AT4G34640", "AT4G30090",
+ "AT5G43460", "AT5G58070", "AT1G07670", "AT1G43910", "AT3G52850",
+ "AT5G27330", "AT1G09330", "AT1G13900", "AT1G28340", "AT1G31130",
+ "AT1G52780", "AT1G53840", "AT2G14720", "AT2G14740", "AT2G34300",
+ "AT3G05710", "AT4G12650", "AT4G30260", "AT5G64030", "AT1G27980",
+ "AT2G32440", "AT1G09870", "AT2G40890", "AT3G28510", "AT4G31500",
+ "AT1G14320", "AT2G09990", "AT2G36160", "AT3G07110", "AT3G18820",
+ "AT3G49360", "AT1G11580", "AT3G54840", "AT4G13940", "AT5G02450",
+ "AT5G19550", "AT1G56070", "AT1G77120", "AT3G15950", "AT3G16460",
+ "AT4G31700", "AT5G10360", "AT1G72370", "AT4G09320", "AT3G04920",
+ "AT5G20290", "AT2G16660", "AT3G03520", "AT3G13080", "AT3G21250",
+ "AT4G38350", "AT5G39040", "AT3G06510", "AT4G11010", "AT5G64290",
+ "AT2G31190", "AT2G38550", "AT3G20390", "AT3G49560", "AT4G00860",
+ "AT4G35000", "AT5G03895", "AT5G14220", "AT5G33320", "AT5G53170",
+ "AT5G64970", "AT1G27950", "AT1G74790", "AT2G01630", "AT2G04780",
+ "AT2G18960", "AT2G37170", "AT2G45470", "AT3G07160", "AT3G07390",
+ "AT3G13560", "AT3G47950", "AT3G60900", "AT4G03550", "AT4G12420",
+ "AT4G12730", "AT4G25240", "AT4G26690", "AT4G27520", "AT4G29900",
+ "AT4G30190", "AT4G31140", "AT4G35100", "AT4G39400", "AT5G55480",
+ "AT5G55730", "AT5G57110", "AT5G58090", "AT5G62670", "AT1G02520",
+ "AT1G11330", "AT1G14870", "AT1G15210", "AT1G16920", "AT1G27190",
+ "AT1G30360", "AT1G56140", "AT2G26300", "AT2G36380", "AT2G36910",
+ "AT2G37050", "AT2G43610", "AT2G45820", "AT2G47000", "AT3G02880",
+ "AT3G08510", "AT3G09740", "AT3G14840", "AT3G17840", "AT3G23750",
+ "AT3G24660", "AT3G25610", "AT3G28450", "AT3G53480", "AT4G08850",
+ "AT4G20830", "AT4G35790", "AT5G04885", "AT5G07910", "AT5G45480",
+ "AT5G49760", "AT5G50000", "AT5G46800", "AT1G10950", "AT1G03220",
+ "AT1G22280", "AT1G59870", "AT2G23810", "AT3G06300", "AT3G25290",
+ "AT3G46290", "AT5G06320", "AT3G11070", "AT5G55610", "AT2G43950",
+ "AT3G08630", "AT5G22640", "AT5G42960", "AT2G36290", "AT5G42980",
+ "AT5G62740", "AT3G52930", "AT5G09810", "AT1G43890", "AT2G32240",
+ "AT3G09630", "AT3G49910", "AT5G64440", "AT2G30860", "AT5G26280",
+ "AT5G27850", "AT2G39480", "AT3G51550", "AT4G35230", "AT5G04930",
+ "AT5G17760", "AT1G07510", "AT3G19340", "AT5G23850", "AT1G24510",
+ "AT2G16060", "AT5G24290", "AT5G26260", "AT2G31390", "AT4G17120",
+ "AT4G17140", "AT4G23850", "AT5G17920", "AT4G25900", "AT1G01610",
+ "AT1G05070", "AT1G05500", "AT1G06840", "AT1G09630", "AT1G10130",
+ "AT1G10290", "AT1G13280", "AT1G14670", "AT1G14830", "AT1G14850",
+ "AT1G17290", "AT1G17500", "AT1G22530", "AT1G29020", "AT1G29980",
+ "AT1G30000", "AT1G32090", "AT1G43170", "AT1G48920", "AT1G54000",
+ "AT1G55160", "AT1G59820", "AT1G64880", "AT1G66270", "AT1G69460",
+ "AT1G69840", "AT1G72090", "AT1G73990", "AT1G76040", "AT1G76270",
+ "AT1G78850", "AT1G80950", "AT2G04280", "AT2G17440", "AT2G17720",
+ "AT2G18193", "AT2G18690", "AT2G20360", "AT2G20450", "AT2G20807",
+ "AT2G26250", "AT2G27490", "AT2G29960", "AT2G30930", "AT2G38530",
+ "AT2G43350", "AT2G47800", "AT3G01290", "AT3G01930", "AT3G02875",
+ "AT3G03060", "AT3G10370", "AT3G10730", "AT3G11730", "AT3G11820",
+ "AT3G18480", "AT3G19820", "AT3G22370", "AT3G23175", "AT3G23400",
+ "AT3G23450", "AT3G24550", "AT3G25780", "AT3G28860", "AT3G43190",
+ "AT3G46830", "AT3G47200", "AT3G49870", "AT3G50930", "AT3G51580",
+ "AT3G51740", "AT3G57020", "AT3G60190", "AT3G61050", "AT3G61440",
+ "AT3G62700", "AT4G00090", "AT4G02930", "AT4G04910", "AT4G11850",
+ "AT4G12590", "AT4G15000", "AT4G16500", "AT4G16650", "AT4G17170",
+ "AT4G18100", "AT4G18430", "AT4G19640", "AT4G20110", "AT4G21700",
+ "AT4G21960", "AT4G23630", "AT4G23650", "AT4G23940", "AT4G25720",
+ "AT4G27500", "AT4G30990", "AT4G31430", "AT4G32410", "AT4G34200",
+ "AT4G34960", "AT4G36750", "AT4G37410", "AT4G37820", "AT4G39030",
+ "AT4G39990", "AT5G02870", "AT5G04480", "AT5G04990", "AT5G08080",
+ "AT5G10840", "AT5G14950", "AT5G15910", "AT5G18280", "AT5G18900",
+ "AT5G19320", "AT5G25100", "AT5G28060", "AT5G39410", "AT5G40480",
+ "AT5G42080", "AT5G44240", "AT5G45130", "AT5G45470", "AT5G45750",
+ "AT5G47910", "AT5G47990", "AT5G48000", "AT5G48030", "AT5G50370",
+ "AT5G56730", "AT5G57800", "AT5G58100", "AT5G63030", "AT5G64100",
+ "AT5G65270", "AT1G66280", "AT1G04120", "AT1G53210", "AT1G63010",
+ "AT2G02040", "AT5G09400", "AT5G39510", "AT5G51570", "AT1G12840",
+ "AT1G15690", "AT1G30400", "AT1G78900", "AT2G21410", "AT2G34660",
+ "AT2G41560", "AT3G28710", "AT3G42050", "AT3G58730", "AT4G11150",
+ "AT4G39080"),
+ 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
51.920 0.408 52.318
MsCoreUtils.Rcheck/MsCoreUtils-Ex.timings
| name | user | system | elapsed | |
| aggregate | 0.624 | 0.078 | 0.702 | |
| binning | 0.001 | 0.000 | 0.001 | |
| breaks_ppm | 0.001 | 0.000 | 0.001 | |
| check | 0 | 0 | 0 | |
| coerce | 0.000 | 0.000 | 0.001 | |
| colCounts | 0 | 0 | 0 | |
| common_path | 0.001 | 0.000 | 0.001 | |
| distance | 0.000 | 0.000 | 0.001 | |
| entropy | 0 | 0 | 0 | |
| estimateBaseline | 0.030 | 0.001 | 0.031 | |
| force_sorted | 0.000 | 0.000 | 0.001 | |
| formatRt | 0.000 | 0.000 | 0.001 | |
| gnps | 0.003 | 0.000 | 0.003 | |
| group | 0.001 | 0.000 | 0.001 | |
| i2index | 0 | 0 | 0 | |
| imputation | 0.004 | 0.002 | 0.006 | |
| localMaxima | 0 | 0 | 0 | |
| matching | 0.001 | 0.001 | 0.001 | |
| maxi | 0 | 0 | 0 | |
| medianPolish | 0.001 | 0.000 | 0.001 | |
| noise | 0.000 | 0.000 | 0.001 | |
| normalize | 0.003 | 0.002 | 0.005 | |
| peakRegionMask | 0 | 0 | 0 | |
| ppm | 0.001 | 0.000 | 0.000 | |
| range | 0 | 0 | 0 | |
| rbindFill | 0.002 | 0.001 | 0.004 | |
| refineCentroids | 0.043 | 0.001 | 0.044 | |
| rla | 0.000 | 0.000 | 0.001 | |
| robustSummary | 0.002 | 0.001 | 0.004 | |
| smooth | 0.006 | 0.000 | 0.006 | |
| sumi | 0.000 | 0.000 | 0.001 | |
| validation | 0 | 0 | 0 | |
| valleys | 0.002 | 0.000 | 0.001 | |
| vapply | 0 | 0 | 0 | |
| which | 0 | 0 | 0 | |