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BioC 3.3: CHECK report for FindMyFriends on oaxaca

This page was generated on 2016-10-13 13:02:09 -0700 (Thu, 13 Oct 2016).

Package 383/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindMyFriends 1.2.2
Thomas Lin Pedersen
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/FindMyFriends
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FindMyFriends
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FindMyFriends_1.2.2.tar.gz
StartedAt: 2016-10-13 01:28:18 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:39:07 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 649.6 seconds
RetCode: 0
Status:  OK 
CheckDir: FindMyFriends.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FindMyFriends_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/FindMyFriends.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.2’
* 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 7.851  0.247   8.257
kmerLink  5.634  0.052   5.725
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/FindMyFriends.Rcheck/00check.log’
for details.

FindMyFriends.Rcheck/00install.out:

* installing *source* package ‘FindMyFriends’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cdhit-bombs.cpp -o cdhit-bombs.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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: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: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: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:1419:21: 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:1418:25: warning: unused variable 'm' [-Wunused-variable]
        int  j, k, j0, j1, k1, m;
                               ^
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: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:2365:6: warning: unused variable 'K' [-Wunused-variable]
        int K = N - 100 * T;
            ^
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: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:2537:17: warning: unused variable 'aap_begin' [-Wunused-variable]
        Vector<INTs> & aap_begin = buf.aap_begin;
                       ^
cdhit-common.cpp:2545:6: warning: unused variable 'j' [-Wunused-variable]
        int j, k, j1, len = seq->size;
            ^
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: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:2978:9: warning: unused variable 'mem_limit' [-Wunused-variable]
        size_t mem_limit = MemoryLimit( mem_need, options );
               ^
cdhit-common.cpp:2949:6: warning: unused variable 'len' [-Wunused-variable]
        int len, len_bound;
            ^
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:2949:11: 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: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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cdhit-est.cpp -o cdhit-est.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cdhit.cpp -o cdhit.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c fastaFunctions.cpp -o fastaFunctions.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c fmf-common.cpp -o fmf-common.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c linearKernel.cpp -o linearKernel.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c neighborhoodSim.cpp -o neighborhoodSim.o
neighborhoodSim.cpp:437:9: warning: unused variable 'maxO' [-Wunused-variable]
    int maxO = 0;
        ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c progress.cpp -o progress.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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-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:

nameusersystemelapsed
addGenomes0.8460.0390.900
addGroupInfo0.1010.0170.119
addOrgInfo0.0870.0170.104
cdhitGrouping3.5210.1894.547
collapseParalogues1.5440.0341.581
defaults0.0740.0170.091
fillDefaults0.0020.0000.002
geneLocation0.2430.0190.262
geneNames0.0890.0180.108
geneWidth0.0800.0160.097
genes0.8030.0210.826
getNeighborhood0.3280.0200.409
getRep0.4300.0240.456
gpcGrouping0.0850.0150.099
graphGrouping0.0670.0140.081
groupInfo0.1020.0140.117
groupNames0.1040.0150.120
groupStat7.8510.2478.257
hasGeneGroups0.1780.0330.212
hasGeneInfo0.3340.0370.382
hasParalogueLinks0.2290.0350.266
kmerLink5.6340.0525.725
kmerSimilarity0.1060.0150.122
kmerSplit0.1450.0160.162
loadPgExample1.1060.1061.262
manualGrouping0.0810.0130.094
nGeneGroups0.1060.0150.121
nGenes0.0890.0190.108
nOrganisms0.3530.0170.371
neighborhoodSplit0.2520.0170.270
orgInfo0.0810.0170.098
orgNames0.0910.0170.110
orgStat0.1520.0200.173
pangenome0.9690.0451.015
pcGraph0.4330.0180.452
pgMatrix0.1180.0160.135
plotEvolution1.0950.0211.118
plotGroup0.2530.0280.281
plotNeighborhood0.3210.0160.337
plotSimilarity3.1210.1033.262
plotStat0.8100.0380.853
plotTree0.4630.0320.598
readAnnot0.9000.0481.403
removeGene0.2090.0230.233
reportGroupChanges0.0010.0010.002
seqToGeneGroup0.1040.0180.347
seqToOrg0.0930.0200.310
translated0.0840.0190.668
variableRegions0.2020.0180.336