Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 683/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fastreeR 1.9.0 (landing page) Anestis Gkanogiannis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the fastreeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fastreeR.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: fastreeR |
Version: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fastreeR_1.9.0.tar.gz |
StartedAt: 2024-06-10 03:30:52 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 03:32:17 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 84.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: fastreeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fastreeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fastreeR_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/fastreeR.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘fastreeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fastreeR’ version ‘1.9.0’ * 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 ‘fastreeR’ 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 whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fasta2dist 5.622 0.506 2.637 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ 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: OK
fastreeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fastreeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘fastreeR’ ... ** using staged installation ** R ** 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 (fastreeR)
fastreeR.Rcheck/tests/spelling.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.362 0.118 0.459
fastreeR.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(fastreeR) > > test_check("fastreeR") VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:51 VCFManager: START READ 16777216 2024/06/10 03:31:52 VCFManager: END READ Processed variants : 4 VCF2TREE : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:52 VCFManager: START READ 2024/06/10 03:31:52 VCFManager: END READ Processed variants : 4 2024/06/10 03:31:52 Distances=3x3 hierarchical method=Complete 3 4 2024/06/10 03:31:53 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:53 Clusters=2 S2 0 1 S1 1 2 S3 1 2 3 4 2024/06/10 03:31:53 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:53 Clusters=2 S2 0 1 S1 1 2 S3 1 2 3 4 2024/06/10 03:31:53 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:53 Clusters=2 S2 0 1 S1 1 2 S3 1 2 3 4 2024/06/10 03:31:53 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:53 Clusters=2 S2 0 1 S1 1 2 S3 1 2 100 1000 2024/06/10 03:31:54 Distances=100x100 hierarchical method=Complete ..cutHeight not given, setting it to 0.0794 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:54 Clusters=36 HG00126 1 5 HG00149 1 5 HG00182 1 5 HG00233 1 5 HG00262 1 5 HG00100 2 5 HG00101 2 5 HG00106 2 5 HG00107 2 5 HG00125 2 5 HG00096 3 5 HG00128 3 5 HG00154 3 5 HG00173 3 5 HG00242 3 5 HG00108 4 4 HG00129 4 4 HG00232 4 4 HG00253 4 4 HG00110 5 4 HG00121 5 4 HG00123 5 4 HG00256 5 4 HG00185 6 4 HG00189 6 4 HG00258 6 4 HG00261 6 4 HG00114 7 3 HG00133 7 3 HG00234 7 3 HG00120 8 3 HG00136 8 3 HG00236 8 3 HG00141 9 3 HG00187 9 3 HG00254 9 3 HG00142 10 3 HG00146 10 3 HG00160 10 3 HG00118 11 3 HG00138 11 3 HG00157 11 3 HG00158 12 3 HG00177 12 3 HG00178 12 3 HG00115 13 3 HG00130 13 3 HG00155 13 3 HG00111 14 3 HG00137 14 3 HG00150 14 3 HG00112 15 3 HG00132 15 3 HG00148 15 3 HG00140 16 3 HG00151 16 3 HG00237 16 3 HG00231 17 3 HG00238 17 3 HG00243 17 3 HG00180 18 3 HG00252 18 3 HG00260 18 3 HG00116 19 3 HG00122 19 3 HG00139 19 3 HG00097 20 2 HG00102 20 2 HG00145 21 2 HG00244 21 2 HG00113 22 2 HG00259 22 2 HG00099 23 2 HG00174 23 2 HG00171 24 2 HG00255 24 2 HG00176 25 2 HG00235 25 2 HG00179 26 2 HG00250 26 2 HG00103 27 2 HG00257 27 2 HG00188 28 2 HG00245 28 2 HG00127 29 2 HG00186 29 2 HG00105 30 2 HG00183 30 2 HG00119 31 2 HG00190 31 2 HG00131 32 2 HG00159 32 2 HG00109 33 2 HG00246 33 2 HG00117 34 2 HG00240 34 2 HG00143 35 2 HG00251 35 2 HG00181 36 2 HG00239 36 2 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:54 VCFManager: START READ 2024/06/10 03:31:54 VCFManager: END READ Processed variants : 4 3 0 2024/06/10 03:31:54 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:54 Clusters=2 S2 0 1 S1 1 2 S3 1 2 3 4 2024/06/10 03:31:54 Distances=3x3 hierarchical method=Complete 100 1000 2024/06/10 03:31:54 Distances=100x100 hierarchical method=Complete VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:54 VCFManager: START READ 2024/06/10 03:31:54 VCFManager: END READ Processed variants : 4 3 0 2024/06/10 03:31:55 Distances=3x3 hierarchical method=Complete FASTA2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:55 FastaManager: START READ CHUNK_SIZE=16777216 2024/06/10 03:31:55 FastaManager: Chunk with 7 lines. 2024/06/10 03:31:55 FastaManager: END READ 2024/06/10 03:31:55 FastaManager: FASTA 2 S2 3 S3 3 S1 FASTA2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:55 FastaManager: START READ 2024/06/10 03:31:55 FastaManager: Chunk with 7 lines. 2 S1 2024/06/10 03:31:55 FastaManager: END READ 2 S2 2024/06/10 03:31:55 FastaManager: FASTA 3 S3 FASTA2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:55 FastaManager: START READ 2024/06/10 03:31:55 FastaManager: Chunk with 7 lines. 2024/06/10 03:31:55 FastaManager: END READ 2 S1 2024/06/10 03:31:55 FastaManager: FASTA 2 S2 3 S3 FASTA2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:55 FastaManager: START READ 2024/06/10 03:31:55 FastaManager: Chunk with 7 lines. 2024/06/10 03:31:55 FastaManager: END READ 2 S1 2 S2 2024/06/10 03:31:55 FastaManager: FASTA 3 S3 FASTA2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:56 FastaManager: START READ 2024/06/10 03:31:56 FastaManager: Chunk with 96 lines. 2024/06/10 03:31:56 FastaManager: END READ 2024/06/10 03:31:56 FastaManager: FASTA 2 contig-202000258 3 contig-73001792 4 contig-198000031 5 contig-13001800 6 contig-366001068 7 contig-295001825 8 contig-100000567 9 contig-237001826 10 contig-15000592 11 contig-168000048 12 contig-620000331 13 contig-573001861 14 contig-30001369 14 contig-12001376 16 contig-201001879 17 contig-11000629 18 contig-364 19 contig-25000365 20 contig-136001638 21 contig-127000661 22 contig-16001175 23 contig-20000917 24 contig-448001924 25 contig-171000141 26 contig-5001683 27 contig-7001201 28 contig-19001684 28 contig-5000427 30 contig-218001938 30 contig-6001939 32 contig-60001206 32 contig-65000152 34 contig-600000955 34 contig-263001217 36 contig-261001227 37 contig-16001959 38 contig-47000966 39 contig-623000970 40 contig-98000731 41 contig-52000465 42 contig-118001491 42 contig-48000188 44 contig-53001003 45 contig-230000764 46 contig-40000768 47 contig-105000229 48 contig-186000247 48 contig-19001776 2024/06/10 03:31:57 CalculateD2ChildTask(41): 50 ..done. 2024/06/10 03:31:58 Clusters=2 S2 0 1 S1 1 2 S3 1 2 ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:58 Clusters=2 S2 0 1 S1 1 2 S3 1 2 ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:58 Clusters=2 S2 0 1 S1 1 2 S3 1 2 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:58 VCFManager: START READ 2024/06/10 03:31:58 VCFManager: END READ Processed variants : 4 3 0 2024/06/10 03:31:58 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:58 Clusters=2 S2 0 1 S1 1 2 S3 1 2 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:58 VCFManager: START READ 2024/06/10 03:31:58 VCFManager: END READ Processed variants : 4 3 0 2024/06/10 03:31:58 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:58 Clusters=2 S2 0 1 S1 1 2 S3 1 2 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:58 VCFManager: START READ 2024/06/10 03:31:58 VCFManager: END READ Processed variants : 4 3 0 2024/06/10 03:31:59 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:59 Clusters=2 S2 0 1 S1 1 2 S3 1 2 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:59 VCFManager: START READ 2024/06/10 03:31:59 VCFManager: END READ Processed variants : 4 3 0 2024/06/10 03:31:59 Distances=3x3 hierarchical method=Complete ..cutHeight not given, setting it to 1.74 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:31:59 Clusters=2 S2 0 1 S1 1 2 S3 1 2 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:31:59 VCFManager: START READ 2024/06/10 03:31:59 VCFManager: END READ Processed variants : 1000 2024/06/10 03:31:59 CalculateDistancesChildTask(89): 50 2024/06/10 03:31:59 CalculateDistancesChildTask(64): 100 100 0 2024/06/10 03:32:00 Distances=100x100 hierarchical method=Complete ..cutHeight not given, setting it to 0.0794 ===> 99% of the (truncated) height range in dendro. ..done. 2024/06/10 03:32:00 Clusters=36 HG00126 1 5 HG00149 1 5 HG00182 1 5 HG00233 1 5 HG00262 1 5 HG00100 2 5 HG00101 2 5 HG00106 2 5 HG00107 2 5 HG00125 2 5 HG00096 3 5 HG00128 3 5 HG00154 3 5 HG00173 3 5 HG00242 3 5 HG00108 4 4 HG00129 4 4 HG00232 4 4 HG00253 4 4 HG00110 5 4 HG00121 5 4 HG00123 5 4 HG00256 5 4 HG00185 6 4 HG00189 6 4 HG00258 6 4 HG00261 6 4 HG00114 7 3 HG00133 7 3 HG00234 7 3 HG00120 8 3 HG00136 8 3 HG00236 8 3 HG00141 9 3 HG00187 9 3 HG00254 9 3 HG00142 10 3 HG00146 10 3 HG00160 10 3 HG00118 11 3 HG00138 11 3 HG00157 11 3 HG00158 12 3 HG00177 12 3 HG00178 12 3 HG00115 13 3 HG00130 13 3 HG00155 13 3 HG00111 14 3 HG00137 14 3 HG00150 14 3 HG00112 15 3 HG00132 15 3 HG00148 15 3 HG00140 16 3 HG00151 16 3 HG00237 16 3 HG00231 17 3 HG00238 17 3 HG00243 17 3 HG00180 18 3 HG00252 18 3 HG00260 18 3 HG00116 19 3 HG00122 19 3 HG00139 19 3 HG00097 20 2 HG00102 20 2 HG00145 21 2 HG00244 21 2 HG00113 22 2 HG00259 22 2 HG00099 23 2 HG00174 23 2 HG00171 24 2 HG00255 24 2 HG00176 25 2 HG00235 25 2 HG00179 26 2 HG00250 26 2 HG00103 27 2 HG00257 27 2 HG00188 28 2 HG00245 28 2 HG00127 29 2 HG00186 29 2 HG00105 30 2 HG00183 30 2 HG00119 31 2 HG00190 31 2 HG00131 32 2 HG00159 32 2 HG00109 33 2 HG00246 33 2 HG00117 34 2 HG00240 34 2 HG00143 35 2 HG00251 35 2 HG00181 36 2 HG00239 36 2 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:32:00 VCFManager: START READ 2024/06/10 03:32:00 VCFManager: END READ Processed variants : 4 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:32:00 VCFManager: START READ 2024/06/10 03:32:00 VCFManager: END READ Processed variants : 4 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:32:00 VCFManager: START READ 2024/06/10 03:32:00 VCFManager: END READ Processed variants : 4 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:32:00 VCFManager: START READ 2024/06/10 03:32:00 VCFManager: END READ Processed variants : 4 VCF2DIST : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:32:01 VCFManager: START READ 2024/06/10 03:32:01 VCFManager: END READ Processed variants : 1000 2024/06/10 03:32:01 CalculateDistancesChildTask(79): 50 2024/06/10 03:32:01 CalculateDistancesChildTask(61): 100 VCF2ISTATS : Sun Jun 09 15:46:01 EDT 2024 Num of Ind = 3 VCF2ISTATS : Sun Jun 09 15:46:01 EDT 2024 Num of Ind = 3 VCF2ISTATS : Sun Jun 09 15:46:01 EDT 2024 Num of Ind = 3 VCF2TREE : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:32:02 VCFManager: START READ 2024/06/10 03:32:02 VCFManager: END READ Processed variants : 4 2024/06/10 03:32:02 Distances=3x3 hierarchical method=Complete VCF2TREE : Sun Jun 09 15:46:01 EDT 2024 cpus=24 using=2 2024/06/10 03:32:02 VCFManager: START READ 2024/06/10 03:32:02 VCFManager: END READ Processed variants : 1000 2024/06/10 03:32:02 CalculateDistancesChildTask(40): 50 2024/06/10 03:32:02 CalculateDistancesChildTask(70): 100 2024/06/10 03:32:02 Distances=100x100 hierarchical method=Complete [ FAIL 0 | WARN 0 | SKIP 0 | PASS 100 ] > > proc.time() user system elapsed 20.819 1.770 13.826
fastreeR.Rcheck/fastreeR-Ex.timings
name | user | system | elapsed | |
dist2clusters | 1.819 | 0.164 | 1.567 | |
dist2tree | 0.363 | 0.028 | 0.227 | |
fasta2dist | 5.622 | 0.506 | 2.637 | |
tree2clusters | 0.271 | 0.021 | 0.233 | |
vcf2clusters | 3.877 | 0.300 | 1.241 | |
vcf2dist | 1.481 | 0.214 | 0.604 | |
vcf2istats | 1.237 | 0.120 | 0.666 | |
vcf2tree | 1.526 | 0.042 | 0.377 | |