Package: FindMyFriends

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FindMyFriends.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FindMyFriends_1.13.0.tar.gz

StartedAt: 2019-04-09 01:54:16 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:04:21 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 605.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: FindMyFriends.Rcheck

Warnings: NA

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FindMyFriends.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FindMyFriends_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FindMyFriends.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.13.0’
* 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 ... WARNING
Functions or methods with usage in documentation object 'pgVirtual-class' but not in code:
  as

* 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
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
groupStat     8.790  0.601   9.490
kmerLink      5.972  0.158   6.268
cdhitGrouping 4.706  0.484   5.197
* 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:
  ── 2. Error: kmerSimilarity works (@test-similarities.R#9)  ────────────────────
  non-numeric argument to binary operator
  1: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam()) at testthat/test-similarities.R:9
  2: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam())
  3: .local(object, ...)
  4: lkParallel(er, pParam, bpworkers(pParam), lowerLimit = lowerLimit)
  5: getChunks(nrow(x), nSplits)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 288 SKIPPED: 1 FAILED: 2
  1. Error: kmerLink works (@test-linking.R#9) 
  2. Error: kmerSimilarity works (@test-similarities.R#9) 
  
  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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/FindMyFriends.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FindMyFriends
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FindMyFriends’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c cdhit-bombs.cpp -o cdhit-bombs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/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:918:14: warning: unused variable 'letters2' [-Wunused-variable]
        const char *letters2 = "ACGTNX";
                    ^
cdhit-common.cpp:917:14: warning: unused variable 'letters' [-Wunused-variable]
        const char *letters = "acgtnx";
                    ^
cdhit-common.cpp:777:6: warning: unused variable 'jj' [-Wunused-variable]
        int jj, kk;
            ^
cdhit-common.cpp:777:10: warning: unused variable 'kk' [-Wunused-variable]
        int jj, kk;
                ^
cdhit-common.cpp:778:6: warning: unused variable 'iden_no1' [-Wunused-variable]
        int iden_no1;
            ^
cdhit-common.cpp:1200:6: warning: unused variable 'i' [-Wunused-variable]
        int i;
            ^
cdhit-common.cpp:1419:6: warning: unused variable 'ix1' [-Wunused-variable]
        int ix1, ix2, ix3, ix4;
            ^
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:1417:6: warning: unused variable 'S' [-Wunused-variable]
        int S = frag_count ? frag_count : sequences.size();
            ^
cdhit-common.cpp:1419:21: warning: unused variable 'ix4' [-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:2329:9: warning: unused variable 'j' [-Wunused-variable]
        int i, j, k;
               ^
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:2338:6: warning: unused variable 'flag' [-Wunused-variable]
        int flag;
            ^
cdhit-common.cpp:2337:11: warning: unused variable 'len_bound' [-Wunused-variable]
        int len, len_bound;
                 ^
cdhit-common.cpp:2365:6: warning: unused variable 'K' [-Wunused-variable]
        int K = N - 100 * T;
            ^
cdhit-common.cpp:2537:17: warning: unused variable 'aap_begin' [-Wunused-variable]
        Vector<INTs> & aap_begin = buf.aap_begin;
                       ^
cdhit-common.cpp:2539:17: warning: unused variable 'taap' [-Wunused-variable]
        Vector<int>  & taap = buf.taap;
                       ^
cdhit-common.cpp:2536:17: warning: unused variable 'aap_list' [-Wunused-variable]
        Vector<INTs> & aap_list = buf.aap_list;
                       ^
cdhit-common.cpp:2579:6: warning: unused variable 'M' [-Wunused-variable]
        int M = frag_size ? table.frag_count : S;
            ^
cdhit-common.cpp:2590:8: warning: unused variable 'lookptr' [-Wunused-variable]
        INTs *lookptr;
              ^
cdhit-common.cpp:2589:6: warning: unused variable 'best1' [-Wunused-variable]
        int best1, sum;
            ^
cdhit-common.cpp:2545:6: warning: unused variable 'j' [-Wunused-variable]
        int j, k, j1, len = seq->size;
            ^
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:2702:17: warning: unused variable 'taap' [-Wunused-variable]
        Vector<int>  & taap = buf.taap;
                       ^
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:2950:6: warning: unused variable 'flag' [-Wunused-variable]
        int flag;
            ^
cdhit-common.cpp:2949:6: warning: unused variable 'len' [-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: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:3145:11: warning: unused variable 'seqi' [-Wunused-variable]
                                char *seqi = seq->data;
                                      ^
cdhit-common.cpp:3097:9: warning: unused variable 'mem_limit' [-Wunused-variable]
        size_t mem_limit = MemoryLimit( mem_need, options );
               ^
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:61:12: warning: unused variable 'aa' [-Wunused-const-variable]
const char aa[] = {"ARNDCQEGHILKMFPSTWYVBZX"};
           ^
58 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c cdhit-est.cpp -o cdhit-est.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c cdhit.cpp -o cdhit.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastaFunctions.cpp -o fastaFunctions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c fmf-common.cpp -o fmf-common.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c linearKernel.cpp -o linearKernel.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c panSim.cpp -o panSim.o
panSim.cpp:19:9: warning: unused variable 'iVal' [-Wunused-variable]
    int iVal;
        ^
panSim.cpp:16:9: warning: unused variable 'k' [-Wunused-variable]
    int k;
        ^
panSim.cpp:20:9: warning: unused variable 'jVal' [-Wunused-variable]
    int jVal;
        ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c progress.cpp -o progress.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c smallgraph.cpp -o smallgraph.o
clang++ -std=gnu++11 -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-FindMyFriends/00new/FindMyFriends/libs
** 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
** 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 (FindMyFriends)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
── 1. Error: kmerLink works (@test-linking.R#9)  ───────────────────────────────
non-numeric argument to binary operator
1: kmerLink(pg, lowerLimit = 0.8, pParam = BiocParallel::SerialParam(), kmerSize = 4) at testthat/test-linking.R:9
2: kmerLink(pg, lowerLimit = 0.8, pParam = BiocParallel::SerialParam(), kmerSize = 4)
3: .local(object, ...)
4: lkParallel(er, pParam, bpworkers(pParam), lowerLimit = lowerLimit)
5: getChunks(nrow(x), nSplits)

── 2. Error: kmerSimilarity works (@test-similarities.R#9)  ────────────────────
non-numeric argument to binary operator
1: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam()) at testthat/test-similarities.R:9
2: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam())
3: .local(object, ...)
4: lkParallel(er, pParam, bpworkers(pParam), lowerLimit = lowerLimit)
5: getChunks(nrow(x), nSplits)

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 288 SKIPPED: 1 FAILED: 2
1. Error: kmerLink works (@test-linking.R#9) 
2. Error: kmerSimilarity works (@test-similarities.R#9) 

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
addGenomes	0.712	0.094	0.819
addGroupInfo	0.201	0.062	0.264
addOrgInfo	0.109	0.042	0.153
cdhitGrouping	4.706	0.484	5.197
collapseParalogues	1.471	0.229	1.699
defaults	0.104	0.041	0.145
fillDefaults	0.005	0.000	0.006
geneLocation	0.328	0.042	0.373
geneNames	0.104	0.046	0.151
geneWidth	0.101	0.048	0.149
genes	0.848	0.060	0.909
getNeighborhood	0.484	0.045	0.530
getRep	0.210	0.041	0.250
gpcGrouping	0.097	0.034	0.130
graphGrouping	0.151	0.052	0.203
groupInfo	0.121	0.049	0.171
groupNames	0.123	0.045	0.168
groupStat	8.790	0.601	9.490
hasGeneGroups	0.214	0.086	0.300
hasGeneInfo	0.365	0.077	0.443
hasParalogueLinks	0.253	0.095	0.347
kmerLink	5.972	0.158	6.268
kmerSimilarity	0.103	0.036	0.139
kmerSplit	0.117	0.037	0.154
loadPgExample	1.171	0.337	1.521
manualGrouping	0.115	0.042	0.171
nGeneGroups	0.124	0.047	0.197
nGenes	0.071	0.028	0.099
nOrganisms	0.077	0.027	0.104
neighborhoodSplit	0.244	0.039	0.284
orgInfo	0.088	0.026	0.114
orgNames	0.101	0.038	0.138
orgStat	0.234	0.046	0.280
pangenome	1.082	0.115	1.197
pcGraph	0.477	0.046	0.525
pgMatrix	0.146	0.037	0.183
plotEvolution	1.523	0.074	1.609
plotGroup	0.271	0.061	0.334
plotNeighborhood	0.450	0.044	0.499
plotSimilarity	2.724	0.084	2.828
plotStat	0.621	0.057	0.701
plotTree	0.581	0.043	0.625
readAnnot	1.134	0.165	1.301
removeGene	0.296	0.049	0.346
reportGroupChanges	0.001	0.000	0.001
seqToGeneGroup	0.143	0.037	0.181
seqToOrg	0.106	0.041	0.147
translated	0.100	0.037	0.137
variableRegions	0.384	0.043	0.428