gap

Package: gap
Version: 1.1-16
Date: 2015-6-6
Title: Genetic Analysis Package
Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and
Brian Ripley
Maintainer: Jing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
Depends: R (>= 2.10)
Suggests: BradleyTerry2, MASS, Matrix, MCMCglmm, R2jags, bdsmatrix,
coda, coxme, foreign, grid, haplo.stats, kinship2, lattice,
magic, mets, nlme, pedigree, pedigreemm, regress, rms, survival
LazyData: Yes
LazyLoad: Yes
Description: It is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it
contains functions for sample size calculations of both
population-based and family-based designs, probability of
familial disease aggregation, kinship calculation, statistics
in linkage analysis, and association analysis involving genetic
markers including haplotype analysis with or without environmental
covariates.
License: GPL (>= 2)
URL: http://www.mrc-epid.cam.ac.uk/people/jing-hua-zhao/
NeedsCompilation: yes
Repository: CRAN
Packaged: 2015-06-05 22:46:42 UTC; jhz22
Date/Publication: 2015-06-06 08:56:06

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'gap' ...
** package 'gap' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c 2k.c -o 2k.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c 2ld.c -o 2ld.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cline.c -o cline.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gcontrol.c -o gcontrol.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gcx.c -o gcx.o
gcx.c: In function 'xehm':
gcx.c:1498:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(record,300,fi);
 ^
gcx.c:1507:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(record,300,fi);
 ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gif.c -o gif.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hap.c -o hap.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hwe.hardy.c -o hwe.hardy.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c kin.morgan.c -o kin.morgan.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c makeped.c -o makeped.o
makeped.c: In function 'read_pedigree':
makeped.c:165:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(stdin,"%s",pedigree_s);
   ^
makeped.c: In function 'read_person':
makeped.c:179:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(stdin,"%s",person_s);
   ^
makeped.c: In function 'getind':
makeped.c:264:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(pedfile,"%s",temp_s);
     ^
makeped.c: In function 'getindpa':
makeped.c:343:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(pedfile,"%s",temp_s);
     ^
makeped.c: In function 'readped':
makeped.c:464:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(pedfile,"%s",newped_s);
   ^
makeped.c:486:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(pedfile,"%d",&sex);
     ^
makeped.c:497:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
         fscanf(pedfile,"%s",newped_s);
         ^
makeped.c: In function 'save_loops':
makeped.c:611:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(stdin,"%1s",&response);
   ^
makeped.c:617:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(loop_file,max_filespec,stdin);
       ^
makeped.c: In function 'file_loops':
makeped.c:813:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
    fscanf(loopf,"%s",pedigree_s);
    ^
makeped.c:814:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
    fscanf(loopf,"%s",person_s);
    ^
makeped.c: In function 'save_probands':
makeped.c:1049:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(stdin,"%1s",&response);
   ^
makeped.c:1055:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(proband_file,max_filespec,stdin);
       ^
makeped.c: In function 'file_probands':
makeped.c:1179:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
        fscanf(prof,"%s",pedigree_s);
        ^
makeped.c:1180:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
        fscanf(prof,"%s",person_s);
        ^
makeped.c: In function 'get_probands':
makeped.c:1411:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(stdin,"%1s",&response);
   ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mia.c -o mia.o
mia.c: In function 'mia':
mia.c:57:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, MAX_LINE_LEN, infile);
       ^
mia.c:99:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, MAX_LINE_LEN, infile);
         ^
mia.c:200:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, MAX_LINE_LEN, infile);
         ^
mia.c:245:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
         fgets(line,MAX_LINE_LEN,infile);
         ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c muvar.c -o muvar.o
f95   -fpic  -g -O2  -c pfc.f -o pfc.o
f95   -fpic  -g -O2  -c pfc.sim.f -o pfc.sim.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pgc.c -o pgc.o
pgc.c: In function 'getloci':
pgc.c:195:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,240,fp);
 ^
pgc.c:202:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,240,fp);
 ^
pgc.c:205:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,240,fp);
 ^
pgc.c:207:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,240,fp);
 ^
pgc.c:210:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,240,fp);
 ^
pgc.c: In function 'getlocim':
pgc.c:435:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,500,fp);
 ^
pgc.c:442:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,500,fp);
 ^
pgc.c:445:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,500,fp);
 ^
pgc.c:447:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,500,fp);
 ^
pgc.c:450:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
 fgets(line,500,fp);
 ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whscore.c -o whscore.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o gap.so 2k.o 2ld.o cline.o gcontrol.o gcx.o gif.o hap.o hwe.hardy.o kin.morgan.o makeped.o mia.o muvar.o pfc.o pfc.sim.o pgc.o whscore.o -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/gap/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gap'
    finding HTML links ... done
    AE3                                     html  
    BFDP                                    html  
    CDKN                                    html  
    ESplot                                  html  
    FPRP                                    html  
    LD22                                    html  
    LDkl                                    html  
    MCMCgrm                                 html  
    PD                                      html  
    SNP                                     html  
    ab                                      html  
    aldh2                                   html  
    apoeapoc                                html  
    asplot                                  html  
    b2r                                     html  
    bt                                      html  
    ccsize                                  html  
    cf                                      html  
    chow.test                               html  
    comp.score                              html  
    crohn                                   html  
    fa                                      html  
    fbsize                                  html  
    fsnps                                   html  
    gap-internal                            html  
    gap-package                             html  
    gc.em                                   html  
    gcontrol                                html  
    gcontrol2                               html  
    gcp                                     html  
    genecounting                            html  
    gif                                     html  
    h2                                      html  
    hap                                     html  
    hap.em                                  html  
    hap.score                               html  
    hla                                     html  
    hr1420                                  html  
    htr                                     html  
    hwe                                     html  
    hwe.cc                                  html  
    hwe.hardy                               html  
    kin.morgan                              html  
    klem                                    html  
    l51                                     html  
    lukas                                   html  
    makeped                                 html  
    mao                                     html  
    masize                                  html  
    metap                                   html  
    metareg                                 html  
    meyer                                   html  
    mfblong                                 html  
    mhtdata                                 html  
    mhtplot                                 html  
    mhtplot2                                html  
    mia                                     html  
    mtdt                                    html  
    mtdt2                                   html  
    muvar                                   html  
    mvmeta                                  html  
    nep499                                  html  
    pbsize                                  html  
    pbsize2                                 html  
    pedtodot                                html  
    pfc                                     html  
    pfc.sim                                 html  
    pgc                                     html  
    plot.hap.score                          html  
    print.hap.score                         html  
    qqfun                                   html  
    qqunif                                  html  
    read.ms.output                          html  
    s2k                                     html  
    tscc                                    html  
    whscore                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gap)
Making 'packages.html' ... done