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BioC 3.4: CHECK report for FindMyFriends on morelia

This page was generated on 2017-04-15 16:26:53 -0400 (Sat, 15 Apr 2017).

Package 416/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindMyFriends 1.4.0
Thomas Lin Pedersen
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/FindMyFriends
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FindMyFriends
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FindMyFriends_1.4.0.tar.gz
StartedAt: 2017-04-15 02:02:33 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 02:12:49 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 616.1 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/FindMyFriends.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 6.339  0.203    6.55
* 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-3.4-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:432:9: 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++ -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 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-3.4-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
addGenomes0.9020.0400.943
addGroupInfo0.1120.0190.131
addOrgInfo0.0790.0160.095
cdhitGrouping3.2740.2153.512
collapseParalogues1.3190.0331.404
defaults0.0650.0150.080
fillDefaults0.0020.0000.002
geneLocation0.2040.0140.217
geneNames0.0740.0130.087
geneWidth0.0950.0140.110
genes0.5990.0170.616
getNeighborhood0.3320.0140.389
getRep0.2200.0170.238
gpcGrouping0.0910.0170.109
graphGrouping0.1030.0180.124
groupInfo0.0950.0140.129
groupNames0.0970.0150.112
groupStat6.3390.2036.550
hasGeneGroups0.1160.0220.137
hasGeneInfo0.2150.0230.238
hasParalogueLinks0.1390.0210.160
kmerLink4.6960.0324.756
kmerSimilarity0.3500.0280.378
kmerSplit0.0840.0180.101
loadPgExample0.6420.0740.789
manualGrouping0.0980.0160.113
nGeneGroups0.0780.0140.093
nGenes0.0710.0140.091
nOrganisms0.0670.0120.131
neighborhoodSplit0.2100.0130.640
orgInfo0.0680.0110.081
orgNames0.0790.0150.094
orgStat0.1470.0120.159
pangenome0.8260.0430.869
pcGraph0.6990.0170.718
pgMatrix0.0840.0140.098
plotEvolution1.0940.0171.122
plotGroup0.2150.0240.238
plotNeighborhood0.2870.0150.302
plotSimilarity3.7670.1043.878
plotStat0.5840.0160.600
plotTree0.5340.0230.559
readAnnot0.9500.0430.996
removeGene0.1940.0170.210
reportGroupChanges0.0010.0010.002
seqToGeneGroup0.0960.0170.113
seqToOrg0.0990.0180.117
translated0.0850.0170.102
variableRegions0.2520.0200.273