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This page was generated on 2017-08-16 13:33:37 -0400 (Wed, 16 Aug 2017).
Package 440/1382 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
FindMyFriends 1.6.0 Thomas Lin Pedersen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ||||||
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
Package: FindMyFriends |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FindMyFriends_1.6.0.tar.gz |
StartedAt: 2017-08-16 02:41:46 -0400 (Wed, 16 Aug 2017) |
EndedAt: 2017-08-16 02:51:53 -0400 (Wed, 16 Aug 2017) |
EllapsedTime: 607.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: FindMyFriends.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FindMyFriends_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/FindMyFriends.Rcheck’ * using R version 3.4.1 (2017-06-30) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FindMyFriends/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FindMyFriends’ version ‘1.6.0’ * 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 ‘FindMyFriends’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘gtable:::insert.unit’ ‘gtable:::z_arrange_gtables’ See the note in ?`:::` about the use of this operator. * 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 ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed groupStat 17.162 0.304 17.821 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: group_data[index[[`_i`]] + 1L, ] <<- value } })() 20: group_data[index[[`_i`]] + 1L, , drop = FALSE] 21: `[.tbl_df`(group_data, index[[`_i`]] + 1L, , drop = FALSE) 22: map(result, `[`, i) 23: lapply(.x, .f, ...) Adding missing grouping variables: `org`, `contig` testthat results ================================================================ OK: 289 SKIPPED: 0 FAILED: 1 1. Error: Groupstatistics works (@test-investigating.R#7) Error: testthat unit tests failed Execution halted * 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: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.5-bioc/meat/FindMyFriends.Rcheck/00check.log’ for details.
testthat.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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. > library(testthat) > library(FindMyFriends) > > test_check("FindMyFriends") Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Also defined by 'filehash' Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Also defined by 'filehash' Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Also defined by 'filehash' 1. Error: Groupstatistics works (@test-investigating.R#7) ---------------------- Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'list' 1: groupStat(pg, 2) at testthat/test-investigating.R:7 2: groupStat(pg, 2) 3: .local(object, ...) 4: info %>% do(groupInfo = { list(maxOrg = max(table(.$organism)), minLength = min(.$width), maxLength = max(.$width), sdLength = sd(.$width), genes = .$gene, backward = if (is.null(.$backward)) NA else .$backward, forward = if (is.null(.$forward)) NA else .$forward) }) %>% arrange_(˜match(geneGroup, groupNames(object))) 5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env)) 6: eval(quote(`_fseq`(`_lhs`)), env, env) 7: eval(quote(`_fseq`(`_lhs`)), env, env) 8: `_fseq`(`_lhs`) 9: freduce(value, `_function_list`) 10: function_list[[i]](value) 11: do(., groupInfo = { list(maxOrg = max(table(.$organism)), minLength = min(.$width), maxLength = max(.$width), sdLength = sd(.$width), genes = .$gene, backward = if (is.null(.$backward)) NA else .$backward, forward = if (is.null(.$forward)) NA else .$forward) }) 12: do.grouped_df(., groupInfo = { list(maxOrg = max(table(.$organism)), minLength = min(.$width), maxLength = max(.$width), sdLength = sd(.$width), genes = .$gene, backward = if (is.null(.$backward)) NA else .$backward, forward = if (is.null(.$forward)) NA else .$forward) }) 13: overscope_eval_next(overscope, args[[j]]) 14: table(.$organism) 15: standardGeneric("table") 16: eval(quote(list(...)), env) 17: eval(quote(list(...)), env) 18: eval(quote(list(...)), env) 19: (function (value) { if (missing(value)) { group_data[index[[`_i`]] + 1L, , drop = FALSE] } else { group_data[index[[`_i`]] + 1L, ] <<- value } })() 20: group_data[index[[`_i`]] + 1L, , drop = FALSE] 21: `[.tbl_df`(group_data, index[[`_i`]] + 1L, , drop = FALSE) 22: map(result, `[`, i) 23: lapply(.x, .f, ...) Adding missing grouping variables: `org`, `contig` testthat results ================================================================ OK: 289 SKIPPED: 0 FAILED: 1 1. Error: Groupstatistics works (@test-investigating.R#7) Error: testthat unit tests failed Execution halted
FindMyFriends.Rcheck/00install.out:
* installing *source* package ‘FindMyFriends’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-bombs.cpp -o cdhit-bombs.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-common.cpp -o cdhit-common.o cdhit-common.cpp:341:9: warning: unused variable 'tm' [-Wunused-variable] time_t tm = time(NULL); ^ cdhit-common.cpp:394:14: warning: unused variable 'message' [-Wunused-variable] const char *message = "Your word length is %i, using %i may be faster!\n"; ^ cdhit-common.cpp:517:8: warning: unused variable 'bip' [-Wunused-variable] INTs *bip; ^ cdhit-common.cpp:866:8: warning: unused variable 's1' [-Wunused-variable] int s1, k0, back; ^ cdhit-common.cpp:866:12: warning: unused variable 'k0' [-Wunused-variable] int s1, k0, back; ^ cdhit-common.cpp:777:6: warning: unused variable 'jj' [-Wunused-variable] int jj, kk; ^ cdhit-common.cpp:778:6: warning: unused variable 'iden_no1' [-Wunused-variable] int iden_no1; ^ cdhit-common.cpp:777:10: warning: unused variable 'kk' [-Wunused-variable] int jj, kk; ^ cdhit-common.cpp:917:14: warning: unused variable 'letters' [-Wunused-variable] const char *letters = "acgtnx"; ^ cdhit-common.cpp:918:14: warning: unused variable 'letters2' [-Wunused-variable] const char *letters2 = "ACGTNX"; ^ cdhit-common.cpp:1200:6: warning: unused variable 'i' [-Wunused-variable] int i; ^ cdhit-common.cpp:1417:6: warning: unused variable 'S' [-Wunused-variable] int S = frag_count ? frag_count : sequences.size(); ^ cdhit-common.cpp:1419:11: warning: unused variable 'ix2' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1419:16: warning: unused variable 'ix3' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1418:25: warning: unused variable 'm' [-Wunused-variable] int j, k, j0, j1, k1, m; ^ cdhit-common.cpp:1419:21: warning: unused variable 'ix4' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1419:6: warning: unused variable 'ix1' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^ cdhit-common.cpp:1469:6: warning: unused variable 'i' [-Wunused-variable] int i; ^ cdhit-common.cpp:1511:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size, n = strlen( s ); ^ cdhit-common.cpp:1517:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size < n ? size : n; ^ cdhit-common.cpp:1533:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size < n ? size : n; ^ cdhit-common.cpp:1622:12: warning: unused variable 'last' [-Wunused-variable] Sequence *last = NULL; ^ cdhit-common.cpp:1755:12: warning: unused variable 'k' [-Wunused-variable] int i, j, k, len; ^ cdhit-common.cpp:1755:9: warning: unused variable 'j' [-Wunused-variable] int i, j, k, len; ^ cdhit-common.cpp:1944:12: warning: unused variable 'k' [-Wunused-variable] int i, k, N = sequences.size(); ^ cdhit-common.cpp:2098:7: warning: unused variable 'k' [-Wunused-variable] int k = len_eff < invd ? len_eff : invd; ^ cdhit-common.cpp:2103:7: warning: unused variable 'ks3' [-Wunused-variable] int ks3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * ss)); ^ cdhit-common.cpp:2104:7: warning: unused variable 'kn3' [-Wunused-variable] int kn3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * NAA)); ^ cdhit-common.cpp:2255:7: warning: unused variable 'size' [-Wunused-variable] int size = rep_seqs.size(); ^ cdhit-common.cpp:2365:6: warning: unused variable 'K' [-Wunused-variable] int K = N - 100 * T; ^ cdhit-common.cpp:2337:11: warning: unused variable 'len_bound' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:2338:6: warning: unused variable 'flag' [-Wunused-variable] int flag; ^ cdhit-common.cpp:2337:6: warning: unused variable 'len' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:2367:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^ cdhit-common.cpp:2329:9: warning: unused variable 'j' [-Wunused-variable] int i, j, k; ^ cdhit-common.cpp:2537:17: warning: unused variable 'aap_begin' [-Wunused-variable] Vector<INTs> & aap_begin = buf.aap_begin; ^ cdhit-common.cpp:2536:17: warning: unused variable 'aap_list' [-Wunused-variable] Vector<INTs> & aap_list = buf.aap_list; ^ cdhit-common.cpp:2589:6: warning: unused variable 'best1' [-Wunused-variable] int best1, sum; ^ cdhit-common.cpp:2590:8: warning: unused variable 'lookptr' [-Wunused-variable] INTs *lookptr; ^ cdhit-common.cpp:2539:17: warning: unused variable 'taap' [-Wunused-variable] Vector<int> & taap = buf.taap; ^ cdhit-common.cpp:2545:6: warning: unused variable 'j' [-Wunused-variable] int j, k, j1, len = seq->size; ^ cdhit-common.cpp:2579:6: warning: unused variable 'M' [-Wunused-variable] int M = frag_size ? table.frag_count : S; ^ cdhit-common.cpp:2702:17: warning: unused variable 'taap' [-Wunused-variable] Vector<int> & taap = buf.taap; ^ cdhit-common.cpp:2699:17: warning: unused variable 'aap_list' [-Wunused-variable] Vector<INTs> & aap_list = buf.aap_list; ^ cdhit-common.cpp:2700:17: warning: unused variable 'aap_begin' [-Wunused-variable] Vector<INTs> & aap_begin = buf.aap_begin; ^ cdhit-common.cpp:2876:55: warning: unused variable 'required_aa1' [-Wunused-variable] int band_width1, band_left, band_center, band_right, required_aa1; ^ cdhit-common.cpp:3024:9: warning: unused variable 'p0' [-Wunused-variable] float p0 = 0; ^ cdhit-common.cpp:2949:11: warning: unused variable 'len_bound' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:2978:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^ cdhit-common.cpp:2950:6: warning: unused variable 'flag' [-Wunused-variable] int flag; ^ cdhit-common.cpp:2979:14: warning: unused variable 'mega' [-Wunused-variable] size_t mem, mega = 1000000; ^ cdhit-common.cpp:2979:9: warning: unused variable 'mem' [-Wunused-variable] size_t mem, mega = 1000000; ^ cdhit-common.cpp:2949:6: warning: unused variable 'len' [-Wunused-variable] int len, len_bound; ^ cdhit-common.cpp:3145:11: warning: unused variable 'seqi' [-Wunused-variable] char *seqi = seq->data; ^ cdhit-common.cpp:3063:9: warning: unused variable 'is' [-Wunused-variable] int i, is, js, flag; ^ cdhit-common.cpp:3063:13: warning: unused variable 'js' [-Wunused-variable] int i, is, js, flag; ^ cdhit-common.cpp:3097:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^ cdhit-common.cpp:61:12: warning: unused variable 'aa' [-Wunused-const-variable] const char aa[] = {"ARNDCQEGHILKMFPSTWYVBZX"}; ^ 58 warnings generated. clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-est.cpp -o cdhit-est.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit.cpp -o cdhit.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c fastaFunctions.cpp -o fastaFunctions.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c fmf-common.cpp -o fmf-common.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c linearKernel.cpp -o linearKernel.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c neighborhoodSim.cpp -o neighborhoodSim.o neighborhoodSim.cpp:432:9: warning: unused variable 'maxO' [-Wunused-variable] int maxO = 0; ^ 1 warning generated. clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c panSim.cpp -o panSim.o panSim.cpp:16:9: warning: unused variable 'k' [-Wunused-variable] int k; ^ panSim.cpp:20:9: warning: unused variable 'jVal' [-Wunused-variable] int jVal; ^ panSim.cpp:19:9: warning: unused variable 'iVal' [-Wunused-variable] int iVal; ^ 3 warnings generated. clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c progress.cpp -o progress.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c smallgraph.cpp -o smallgraph.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FindMyFriends.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o fastaFunctions.o fmf-common.o linearKernel.o neighborhoodSim.o panSim.o progress.o smallgraph.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.5-bioc/meat/FindMyFriends.Rcheck/FindMyFriends/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (FindMyFriends)
FindMyFriends.Rcheck/FindMyFriends-Ex.timings:
name | user | system | elapsed | |
addGenomes | 0.804 | 0.045 | 0.884 | |
addGroupInfo | 0.131 | 0.016 | 0.147 | |
addOrgInfo | 0.068 | 0.016 | 0.094 | |
cdhitGrouping | 3.099 | 0.166 | 3.344 | |
collapseParalogues | 1.094 | 0.033 | 1.184 | |
defaults | 0.056 | 0.012 | 0.069 | |
fillDefaults | 0.005 | 0.000 | 0.005 | |
geneLocation | 0.217 | 0.013 | 0.235 | |
geneNames | 0.073 | 0.014 | 0.088 | |
geneWidth | 0.068 | 0.015 | 0.084 | |
genes | 0.643 | 0.021 | 0.685 | |
getNeighborhood | 0.370 | 0.015 | 0.397 | |
getRep | 0.111 | 0.015 | 0.126 | |
gpcGrouping | 0.050 | 0.010 | 0.074 | |
graphGrouping | 0.057 | 0.011 | 0.067 | |
groupInfo | 0.058 | 0.009 | 0.069 | |
groupNames | 0.059 | 0.010 | 0.069 | |
groupStat | 17.162 | 0.304 | 17.821 | |
hasGeneGroups | 0.126 | 0.026 | 0.156 | |
hasGeneInfo | 0.239 | 0.027 | 0.280 | |
hasParalogueLinks | 0.162 | 0.027 | 0.189 | |
kmerLink | 4.698 | 0.051 | 4.862 | |
kmerSimilarity | 0.058 | 0.012 | 0.075 | |
kmerSplit | 0.105 | 0.012 | 0.117 | |
loadPgExample | 0.679 | 0.083 | 0.784 | |
manualGrouping | 0.069 | 0.013 | 0.091 | |
nGeneGroups | 0.079 | 0.013 | 0.099 | |
nGenes | 0.063 | 0.014 | 0.077 | |
nOrganisms | 0.057 | 0.013 | 0.070 | |
neighborhoodSplit | 0.186 | 0.012 | 0.199 | |
orgInfo | 0.060 | 0.012 | 0.072 | |
orgNames | 0.060 | 0.013 | 0.073 | |
orgStat | 0.122 | 0.013 | 0.137 | |
pangenome | 0.708 | 0.037 | 0.758 | |
pcGraph | 0.334 | 0.015 | 0.351 | |
pgMatrix | 0.098 | 0.012 | 0.114 | |
plotEvolution | 2.294 | 0.021 | 2.383 | |
plotGroup | 0.682 | 0.026 | 0.719 | |
plotNeighborhood | 1.243 | 0.020 | 1.289 | |
plotSimilarity | 3.540 | 0.084 | 3.696 | |
plotStat | 0.603 | 0.014 | 0.642 | |
plotTree | 0.459 | 0.018 | 0.484 | |
readAnnot | 0.659 | 0.034 | 0.712 | |
removeGene | 0.215 | 0.019 | 0.237 | |
reportGroupChanges | 0.043 | 0.000 | 0.044 | |
seqToGeneGroup | 0.077 | 0.016 | 0.095 | |
seqToOrg | 0.101 | 0.015 | 0.117 | |
translated | 0.073 | 0.014 | 0.088 | |
variableRegions | 0.218 | 0.014 | 0.239 | |