Package: FindMyFriends

Version: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2020-04-15 02:17:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:27:04 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 557.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FindMyFriends.Rcheck

Warnings: 1

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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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/FindMyFriends.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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 ‘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 12.260  0.335  12.717
kmerLink   5.599  0.068   5.700
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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:917:14: warning: unused variable 'letters' [-Wunused-variable]
        const char *letters = "acgtnx";
                    ^
cdhit-common.cpp:777:10: warning: unused variable 'kk' [-Wunused-variable]
        int jj, kk;
                ^
cdhit-common.cpp:918:14: warning: unused variable 'letters2' [-Wunused-variable]
        const char *letters2 = "ACGTNX";
                    ^
cdhit-common.cpp:778:6: warning: unused variable 'iden_no1' [-Wunused-variable]
        int iden_no1;
            ^
cdhit-common.cpp:777:6: warning: unused variable 'jj' [-Wunused-variable]
        int jj, kk;
            ^
cdhit-common.cpp:1200:6: warning: unused variable 'i' [-Wunused-variable]
        int i;
            ^
cdhit-common.cpp:1419:21: warning: unused variable 'ix4' [-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:1419:11: warning: unused variable 'ix2' [-Wunused-variable]
        int ix1, ix2, ix3, ix4;
                 ^
cdhit-common.cpp:1417:6: warning: unused variable 'S' [-Wunused-variable]
        int S = frag_count ? frag_count : sequences.size();
            ^
cdhit-common.cpp:1419:6: warning: unused variable 'ix1' [-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: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:2337:11: warning: unused variable 'len_bound' [-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:2365:6: warning: unused variable 'K' [-Wunused-variable]
        int K = N - 100 * T;
            ^
cdhit-common.cpp:2545:6: warning: unused variable 'j' [-Wunused-variable]
        int j, k, j1, len = seq->size;
            ^
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: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: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: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: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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 295 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
327.287   5.028 334.760 

name	user	system	elapsed
addGenomes	1.009	0.051	1.071
addGroupInfo	0.100	0.016	0.118
addOrgInfo	0.073	0.017	0.090
cdhitGrouping	3.283	0.255	3.565
collapseParalogues	1.112	0.074	1.196
defaults	0.082	0.018	0.102
fillDefaults	0.003	0.000	0.004
geneLocation	0.247	0.019	0.267
geneNames	0.106	0.018	0.125
geneWidth	0.073	0.016	0.089
genes	0.643	0.021	0.666
getNeighborhood	0.338	0.025	0.369
getRep	0.145	0.016	0.162
gpcGrouping	0.068	0.014	0.081
graphGrouping	0.081	0.020	0.102
groupInfo	0.087	0.019	0.106
groupNames	0.111	0.019	0.130
groupStat	12.260	0.335	12.717
hasGeneGroups	0.165	0.034	0.200
hasGeneInfo	0.325	0.044	0.370
hasParalogueLinks	0.168	0.041	0.215
kmerLink	5.599	0.068	5.700
kmerSimilarity	0.132	0.025	0.158
kmerSplit	0.100	0.023	0.123
loadPgExample	0.900	0.117	1.025
manualGrouping	0.119	0.019	0.138
nGeneGroups	0.092	0.019	0.113
nGenes	0.076	0.022	0.098
nOrganisms	0.081	0.016	0.097
neighborhoodSplit	0.261	0.019	0.280
orgInfo	0.096	0.022	0.129
orgNames	0.080	0.017	0.098
orgStat	0.205	0.024	0.234
pangenome	1.285	0.080	1.403
pcGraph	0.863	0.025	0.903
pgMatrix	0.096	0.019	0.119
plotEvolution	1.762	0.047	1.843
plotGroup	0.244	0.037	0.285
plotNeighborhood	0.330	0.022	0.356
plotSimilarity	1.876	0.062	2.001
plotStat	0.824	0.057	0.894
plotTree	0.551	0.031	0.589
readAnnot	0.838	0.070	0.932
removeGene	0.302	0.031	0.347
reportGroupChanges	0.000	0.000	0.001
seqToGeneGroup	0.102	0.026	0.130
seqToOrg	0.104	0.024	0.128
translated	0.138	0.025	0.168
variableRegions	0.306	0.023	0.340