Erik Wright
| Snapshot Date: 2025-12-22 13:40 -0500 (Mon, 22 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: devel |
| git_last_commit: 9fb2779 |
| git_last_commit_date: 2025-10-29 10:09:13 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-23 11:34 -0500 (Tue, 23 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4878 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 528/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 3.7.0 (landing page) Erik Wright
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the DECIPHER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DECIPHER.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: DECIPHER |
| Version: 3.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DECIPHER_3.7.0.tar.gz |
| StartedAt: 2025-12-22 22:31:06 -0500 (Mon, 22 Dec 2025) |
| EndedAt: 2025-12-22 23:06:51 -0500 (Mon, 22 Dec 2025) |
| EllapsedTime: 2145.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DECIPHER_3.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/DECIPHER.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.7.0’
* 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 ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 12.5Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.6Mb
extdata 1.9Mb
libs 1.1Mb
* 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 code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
Treeline: multiple local function definitions for ‘.NNI’ with different
formal arguments
Treeline: multiple local function definitions for ‘.minimize’ with
different formal arguments
Undefined global functions or variables:
deltaGrulesRNA deltaHrules deltaHrulesRNA
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AlignSeqs 193.127 1.203 194.340
LearnNonCoding 115.699 4.403 120.109
FindNonCoding 60.997 0.613 61.615
Treeline 59.380 0.296 59.679
ExtractGenes 38.961 0.642 39.608
InferSelection 38.109 0.095 38.206
FindGenes 36.762 0.598 37.362
Genes-class 35.859 0.264 36.124
WriteGenes 33.245 0.451 33.698
BrowseSeqs 24.230 0.159 24.392
DistanceMatrix 23.073 0.160 23.237
InferRecombination 18.838 0.063 18.902
CorrectFrameshifts 16.263 0.100 16.363
StaggerAlignment 12.183 0.153 12.338
AlignTranslation 11.516 0.092 11.609
DetectRepeats 11.354 0.096 11.472
Taxa-class 9.810 0.087 9.898
TrimDNA 9.765 0.124 9.891
IdTaxa 9.163 0.030 9.194
InferDemography 8.798 0.018 8.817
Clusterize 8.304 0.063 8.368
LearnTaxa 6.268 0.643 6.911
Array2Matrix 5.201 0.064 5.265
DesignArray 5.225 0.035 5.261
ScoreAlignment 5.143 0.061 5.206
AlignPairs 4.899 0.149 5.053
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
DECIPHER.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DECIPHER
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘DECIPHER’ ...
** this is package ‘DECIPHER’ version ‘3.7.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:438:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized]
438 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:62:51: note: ‘lGs’ was declared here
62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c:436:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized]
436 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:62:46: note: ‘lGp’ was declared here
62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1291:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized]
1291 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:820:51: note: ‘lGs’ was declared here
820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c:1289:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized]
1289 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:820:46: note: ‘lGp’ was declared here
820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:389:25: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized]
389 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(NTHREADS)
| ^~~
AlignProfiles.c:82:17: note: ‘subM’ was declared here
82 | double *subM;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c AssignIndels.c -o AssignIndels.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
CalculateDeltaG.c:463:36: warning: ‘s1’ may be used uninitialized [-Wmaybe-uninitialized]
463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
| ~~~~^~~~~
CalculateDeltaG.c:375:29: note: ‘s1’ was declared here
375 | int i, j, k, count, s1, s2;
| ^~
CalculateDeltaG.c:463:49: warning: ‘s2’ may be used uninitialized [-Wmaybe-uninitialized]
463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
| ~~~~^~~~~
CalculateDeltaG.c:375:33: note: ‘s2’ was declared here
375 | int i, j, k, count, s1, s2;
| ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces]
25 | double dH_DR[4][4] = {
| ^
26 | -11.5, -7.8, -7, -8.3,
| { }
27 | -10.4, -12.8, -16.3, -9.1,
| { }
28 | -8.6, -8, -9.3, -5.9,
| { }
29 | -7.8, -5.5, -9, -7.8
| {
30 | };
| }
CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces]
31 | double dS_DR[4][4] = {
| ^
32 | -36.4, -21.6, -19.7, -23.9,
| { }
33 | -28.4, -31.9, -47.1, -23.5,
| { }
34 | -22.9, -17.1, -23.2, -12.3,
| { }
35 | -23.2, -13.5, -26.1, -21.9
| {
36 | };
| }
CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces]
37 | double dH_DD[4][4] = {
| ^
38 | -7.9, -8.4, -7.8, -7.2,
| { }
39 | -8.5, -8, -10.6, -7.8,
| { }
40 | -8.2, -9.8, -8, -8.4,
| { }
41 | -7.2, -8.2, -8.5, -7.9
| {
42 | };
| }
CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces]
43 | double dS_DD[4][4] = {
| ^
44 | -22.2, -22.4, -21, -20.4,
| { }
45 | -22.7, -19.9, -27.2, -21,
| { }
46 | -22.2, -24.4, -19.9, -22.4,
| { }
47 | -21.3, -22.2, -22.7, -22.2
| {
48 | };
| }
CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces]
49 | double dH_RR[4][4] = {
| ^
50 | -6.6, -10.17, -7.65, -5.76,
| { }
51 | -10.56, -12.21, -7.95, -7.65,
| { }
52 | -13.37, -14.21, -12.21, -10.17,
| { }
53 | -8.11, -13.37, -10.56, -6.6
| {
54 | };
| }
CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces]
55 | double dS_RR[4][4] = {
| ^
56 | -18.38, -26.03, -19.18, -15.67,
| { }
57 | -28.25, -30.02, -19.18, -19.18,
| { }
58 | -35.68, -34.85, -30.02, -26.03,
| { }
59 | -22.59, -35.68, -28.25, -18.38
| {
60 | };
| }
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ChainSegments.c -o ChainSegments.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:439:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
439 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:469:50: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
469 | minCs[i] = minC;
| ~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function ‘cluster._omp_fn.2’:
Cluster.c:493:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
493 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:848:44: warning: ‘minCols’ may be used uninitialized [-Wmaybe-uninitialized]
848 | if (minCols[rowIndices[i]] == (minRow + 1)) {
| ^
Cluster.c:277:14: note: ‘minCols’ was declared here
277 | int *minCols;
| ^~~~~~~
Cluster.c:459:41: warning: ‘nDiv’ may be used uninitialized [-Wmaybe-uninitialized]
459 | #pragma omp parallel for private(i,j,minC,minH) schedule(guided) num_threads(nthreads)
| ^~~
Cluster.c:283:17: note: ‘nDiv’ was declared here
283 | double *nDiv;
| ^~~~
Cluster.c:413:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
413 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ClusterME.c -o ClusterME.o
ClusterME.c: In function ‘clusterME’:
ClusterME.c:322:101: warning: ‘LLRL’ may be used uninitialized [-Wmaybe-uninitialized]
322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac
| ~~~~~^~~~~~
ClusterME.c:284:24: note: ‘LLRL’ was declared here
284 | double LLRL, LRRL, LLRR, LRRR;
| ^~~~
ClusterME.c:322:101: warning: ‘LRRL’ may be used uninitialized [-Wmaybe-uninitialized]
322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac
| ~~~~~^~~~~~
ClusterME.c:284:30: note: ‘LRRL’ was declared here
284 | double LLRL, LRRL, LLRR, LRRR;
| ^~~~
ClusterME.c:323:101: warning: ‘LLRR’ may be used uninitialized [-Wmaybe-uninitialized]
323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc
| ~~~~~^~~~~~
ClusterME.c:284:36: note: ‘LLRR’ was declared here
284 | double LLRL, LRRL, LLRR, LRRR;
| ^~~~
ClusterME.c:323:101: warning: ‘LRRR’ may be used uninitialized [-Wmaybe-uninitialized]
323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc
| ~~~~~^~~~~~
ClusterME.c:284:42: note: ‘LRRR’ was declared here
284 | double LLRL, LRRL, LLRR, LRRR;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ClusterML.c -o ClusterML.o
ClusterML.c: In function ‘clusterML’:
ClusterML.c:2045:17: warning: ‘node’ may be used uninitialized [-Wmaybe-uninitialized]
2045 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
| ^~~
ClusterML.c:1913:17: note: ‘node’ was declared here
1913 | double *node;
| ^~~~
ClusterML.c:2045:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized]
2045 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
| ^~~
ClusterML.c:1959:14: note: ‘Up’ was declared here
1959 | int *Up;
| ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:190:71: warning: ‘temp_nodes’ may be used uninitialized [-Wmaybe-uninitialized]
190 | temp_nodes[j] = 0;
| ~~~~~~~~~~~~~~^~~
ClusterMP.c:163:34: note: ‘temp_nodes’ was declared here
163 | int *temp_subM, *temp_nodes;
| ^~~~~~~~~~
ClusterMP.c:465:49: warning: ‘temp_lengths’ may be used uninitialized [-Wmaybe-uninitialized]
465 | *(temp_lengths + j) += *(S + w*c + m)*weight;
| ^~~~~~~~~~~~~~~~~~~
ClusterMP.c:162:38: note: ‘temp_lengths’ was declared here
162 | double *temp_score, *temp_lengths;
| ^~~~~~~~~~~~
ClusterMP.c:485:73: warning: ‘temp_subM’ may be used uninitialized [-Wmaybe-uninitialized]
485 | *(temp_subM + c*m + w - 1) += weight;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:163:22: note: ‘temp_subM’ was declared here
163 | int *temp_subM, *temp_nodes;
| ^~~~~~~~~
ClusterMP.c:202:49: warning: ‘P’ may be used uninitialized [-Wmaybe-uninitialized]
202 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:185:38: note: ‘P’ was declared here
185 | int *P;
| ^
ClusterMP.c:385:61: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized]
385 | *(R + 3*c*n + m) = 0;
| ^
ClusterMP.c:105:22: note: ‘m’ was declared here
105 | int i, j, k, m, w;
| ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:159:17: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized]
159 | #pragma omp parallel num_threads(nthreads)
| ^~~
ClusterMP.c:128:17: note: ‘lengths’ was declared here
128 | double *lengths, *score;
| ^~~~~~~
ClusterMP.c:159:17: warning: ‘nodes’ may be used uninitialized [-Wmaybe-uninitialized]
159 | #pragma omp parallel num_threads(nthreads)
| ^~~
ClusterMP.c:129:20: note: ‘nodes’ was declared here
129 | int size, *nodes, *subM;
| ^~~~~
ClusterMP.c:159:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized]
159 | #pragma omp parallel num_threads(nthreads)
| ^~~
ClusterMP.c:129:28: note: ‘subM’ was declared here
129 | int size, *nodes, *subM;
| ^~~~
ClusterMP.c:159:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized]
159 | #pragma omp parallel num_threads(nthreads)
| ^~~
ClusterMP.c:145:14: note: ‘Up’ was declared here
145 | int *Up;
| ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Compositions.c -o Compositions.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:1328:25: warning: ‘dict’ may be used uninitialized [-Wmaybe-uninitialized]
1328 | free(dict);
| ^~~~~~~~~~
Compression.c:545:31: note: ‘dict’ was declared here
545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1242:71: warning: ‘lastTriplet’ may be used uninitialized [-Wmaybe-uninitialized]
1242 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
| ~~~^~~~~~~~~~~~~~
Compression.c:632:26: note: ‘lastTriplet’ was declared here
632 | int run, lastTriplet, lastCase;
| ^~~~~~~~~~~
Compression.c:1012:62: warning: ‘word’ may be used uninitialized [-Wmaybe-uninitialized]
1012 | word = (word << 8) | (unsigned int)reorder(byte);
| ~~~~~~^~~~~
Compression.c:545:37: note: ‘word’ was declared here
545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1013:54: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized]
1013 | count++;
| ~~~~~^~
Compression.c:545:43: note: ‘count’ was declared here
545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~
Compression.c:546:41: warning: ‘rev’ may be used uninitialized [-Wmaybe-uninitialized]
546 | int lastTemp, currTemp, rev, len, len2, thresh = 1;
| ^~~
Compression.c:1216:58: warning: ‘lastHit’ may be used uninitialized [-Wmaybe-uninitialized]
1216 | p[c++] = (unsigned char)lastHit;
| ^~~~~~~~~~~~~~~~~~~~~~
Compression.c:545:50: note: ‘lastHit’ was declared here
545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ConsensusSequence.c -o ConsensusSequence.o
In function ‘runsAA’,
inlined from ‘consensusProfileAA’ at ConsensusSequence.c:1836:3:
ConsensusSequence.c:454:50: warning: ‘lastPos’ may be used uninitialized [-Wmaybe-uninitialized]
454 | if (lastGap < (s - 2)) // ensure continuity before the run
| ~~~^~~~
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:397:30: note: ‘lastPos’ was declared here
397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
| ^~~~~~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:1940:17: warning: ‘DBN’ may be used uninitialized [-Wmaybe-uninitialized]
1940 | double *DBN, *s;
| ^~~
ConsensusSequence.c:1941:27: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized]
1941 | int do_DBN, n, l, d;
| ^
ConsensusSequence.c:2043:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized]
2043 | if (tGaps && curr > 0) {
| ~~~~~~^~~~~~~~~~~
ConsensusSequence.c:1930:37: note: ‘curr’ was declared here
1930 | double weight, total, prev, curr;
| ^~~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2083:17: warning: ‘HEC’ may be used uninitialized [-Wmaybe-uninitialized]
2083 | double *HEC, *s;
| ^~~
ConsensusSequence.c:2084:27: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized]
2084 | int do_HEC, n, l, d;
| ^
ConsensusSequence.c:2186:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized]
2186 | if (tGaps && curr > 0) {
| ~~~~~~^~~~~~~~~~~
ConsensusSequence.c:2073:37: note: ‘curr’ was declared here
2073 | double weight, total, prev, curr;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:71:27: warning: missing braces around initializer [-Wmissing-braces]
71 | double NN[4][4] = {
| ^
72 | -0.816507461,-2.5401714,-1.647430026,-1.184658548
| {
73 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
| }{
74 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
| }{
75 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
| }{
76 | };
| }
DesignProbes.c:78:27: warning: missing braces around initializer [-Wmissing-braces]
78 | double PM[4][4] = {
| ^
79 | -0.141370102,-0.439805276,-0.285236035,-0.205111781
| {
80 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
| }{
81 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
| }{
82 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
| }{
83 | };
| }
DesignProbes.c:85:34: warning: missing braces around initializer [-Wmissing-braces]
85 | double sMM[4][5][5][4] = {
| ^
86 | 0,0,0,0
| {{{
87 | ,1.545032445,1.254355018,1.491691514,1.329138183
| }{
88 | ,1.150635633,0.582415494,1.075877275,1.187937642
| }{
89 | ,1.203555051,1.001540513,0.864287715,0.717125848
| }{
90 | ,0.75,0.65,0.69,0.78
| }{
91 | ,0.630005348,0.18553379,0.730763505,0.709272397
| -
| }},{{
92 | ,0,0,0,0
| }{
93 | ,0.856582783,-0.143236405,0.716721488,0.603652831
| }{
94 | ,0.851622883,0.653168672,0.676545316,1.187937642
| }{
95 | ,0.75,0.65,0.69,0.78
| }{
96 | ,1.231861002,0.746214538,1.087821916,0.989140748
| -
| }},{{
97 | ,1.822113278,1.270687029,1.336192565,1.364584949
| }{
98 | ,0,0,0,0
| }{
99 | ,1.443665704,1.385046493,1.256013166,1.329138183
| }{
100 | ,0.75,0.65,0.69,0.78
| }{
101 | ,1.478009492,0.882097231,1.20450984,1.061002478
| -
| }},{{
102 | ,1.496720812,0.846496194,0.967868114,0.989140748
| }{
103 | ,0.766581547,-0.024857805,0.50754303,0.709272397
| }{
104 | ,0,0,0,0
| }{
105 | ,0.75,0.65,0.69,0.78
| }{
106 | ,0.75,0.65,0.69,0.78
| -
| }},{{
107 | ,0.75,0.65,0.69,0.78
| }{
108 | ,0.75,0.65,0.69,0.78
| }{
109 | ,0.76,0.65,0.69,0.78
| }{
110 | ,0,0,0,0
| }{
111 | ,0,0,0,0
| -
| }}},{{{
112 | ,1.295827995,0.84547091,0.91019099,1.256013166
| }{
113 | ,0.755889609,0.241428373,0.396379912,0.676545316
| }{
114 | ,0.99945386,0.740323132,0.435659206,0.864287715
| }{
115 | ,0.65,0.55,0.48,0.69
| }{
116 | ,0.843147406,0.101248351,0.49063599,0.50754303
| -
| }},{{
117 | ,0,0,0,0
| }{
118 | ,1.0651638,0.249934344,0.699352949,0.716721488
| }{
119 | ,0.871921533,0.59458138,0.396379912,1.075877275
| }{
120 | ,0.65,0.56,0.49,0.69
| }{
121 | ,1.07531714,0.318907854,0.653287717,0.967868114
| -
| }},{{
122 | ,1.099899195,0.730184613,0.661798984,1.336192565
| }{
123 | ,0,0,0,0
| }{
124 | ,1.45897431,1.318532145,0.91019099,1.491691514
| }{
125 | ,0.65,0.56,0.49,0.69
| }{
126 | ,1.242135174,0.894838095,1.108555445,1.20450984
| -
| }},{{
127 | ,0.911428974,0.524430101,0.653287717,1.087821916
| }{
128 | ,0.503209827,0.274849491,0.49063599,0.730763505
| }{
129 | ,0,0,0,0
| }{
130 | ,0.65,0.55,0.48,0.69
| }{
131 | ,0.65,0.55,0.48,0.69
| -
| }},{{
132 | ,0.65,0.56,0.49,0.69
| }{
133 | ,0.65,0.56,0.49,0.69
| }{
134 | ,0.65,0.55,0.48,0.69
| }{
135 | ,0,0,0,0
| }{
136 | ,0,0,0,0
| -
| }}},{{{
137 | ,1.100661785,0.969784756,1.318532145,1.385046493
| }{
138 | ,0.565895968,-0.060347902,0.59458138,0.653168672
| }{
139 | ,0.782168488,0.788161238,0.740323132,1.001540513
| }{
140 | ,0.68,0.46,0.55,0.65
| }{
141 | ,0.468913405,-0.469855984,0.274849491,-0.024857805
| -
| }},{{
142 | ,0,0,0,0
| }{
143 | ,0.258195131,-0.70438632,0.249934344,-0.143236405
| }{
144 | ,0.502914193,-0.060347902,0.241428373,0.582415494
| }{
145 | ,0.68,0.47,0.56,0.65
| }{
146 | ,0.584083861,0.258975454,0.524430101,0.846496194
| -
| }},{{
147 | ,0.968040559,0.797499702,0.730184613,1.270687029
| }{
148 | ,0,0,0,0
| }{
149 | ,1.081040749,0.969784756,0.84547091,1.254355018
| }{
150 | ,0.68,0.47,0.56,0.65
| }{
151 | ,1.048553951,0.728354541,0.894838095,0.882097231
| -
| }},{{
152 | ,0.88611252,0.258975454,0.318907854,0.746214538
| }{
153 | ,0.239520858,-0.469855984,0.101248351,0.18553379
| }{
154 | ,0,0,0,0
| }{
155 | ,0.68,0.46,0.55,0.65
| }{
156 | ,0.68,0.46,0.55,0.65
| -
| }},{{
157 | ,0.68,0.47,0.56,0.65
| }{
158 | ,0.68,0.47,0.56,0.65
| }{
159 | ,0.68,0.46,0.55,0.65
| }{
160 | ,0,0,0,0
| }{
161 | ,0,0,0,0
| -
| }}},{{{
162 | ,1.566899704,1.081040749,1.45897431,1.443665704
| }{
163 | ,0.976725675,0.502914193,0.871921533,0.851622883
| }{
164 | ,1.482046826,0.782168488,0.99945386,1.203555051
| }{
165 | ,0.85,0.68,0.65,0.76
| }{
166 | ,0.798628781,0.239520858,0.503209827,0.766581547
| -
| }},{{
167 | ,0,0,0,0
| }{
168 | ,1.141098246,0.258195131,1.0651638,0.856582783
| }{
169 | ,0.976725675,0.565895968,0.755889609,1.150635633
| }{
170 | ,0.85,0.68,0.65,0.75
| }{
171 | ,1.125403302,0.88611252,0.911428974,1.496720812
| -
| }},{{
172 | ,1.68169282,0.968040559,1.099899195,1.822113278
| }{
173 | ,0,0,0,0
| }{
174 | ,1.566899704,1.100661785,1.295827995,1.545032445
| }{
175 | ,0.85,0.68,0.65,0.75
| }{
176 | ,1.35948517,1.048553951,1.242135174,1.478009492
| -
| }},{{
177 | ,1.125403302,0.584083861,1.07531714,1.231861002
| }{
178 | ,0.798628781,0.468913405,0.843147406,0.630005348
| }{
179 | ,0,0,0,0
| }{
180 | ,0.85,0.68,0.65,0.75
| }{
181 | ,0.85,0.68,0.65,0.75
| -
| }},{{
182 | ,0.85,0.68,0.65,0.75
| }{
183 | ,0.85,0.68,0.65,0.75
| }{
184 | ,0.85,0.68,0.65,0.75
| }{
185 | ,0,0,0,0
| }{
186 | };
| }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:838:60: warning: ‘lastCycle’ may be used uninitialized [-Wmaybe-uninitialized]
838 | if (thisCycle < lastCycle) {
| ^
DesignProbes.c:270:58: note: ‘lastCycle’ was declared here
270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
DesignProbes.c:838:60: warning: ‘thisCycle’ may be used uninitialized [-Wmaybe-uninitialized]
838 | if (thisCycle < lastCycle) {
| ^
DesignProbes.c:270:69: note: ‘thisCycle’ was declared here
270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Diff.c -o Diff.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:1009:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
1009 | if (!ci)
| ^~
DistanceMatrix.c:1012:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
1012 | while (i < ex) {
| ^~~~~
DistanceMatrix.c:1031:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
1031 | if (!cj)
| ^~
DistanceMatrix.c:1034:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
1034 | while (j < ey) {
| ^~~~~
DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’:
DistanceMatrix.c:1587:66: warning: ‘OV’ may be used uninitialized [-Wmaybe-uninitialized]
1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:1096:92: note: ‘OV’ was declared here
1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^~
DistanceMatrix.c:1587:66: warning: ‘off’ may be used uninitialized [-Wmaybe-uninitialized]
1587 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:1096:96: note: ‘off’ was declared here
1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^~~
DistanceMatrix.c:1266:53: warning: ‘one’ may be used uninitialized [-Wmaybe-uninitialized]
1266 | two != one) {
| ~~~~^~~~~~
DistanceMatrix.c:1241:29: note: ‘one’ was declared here
1241 | int one, two;
| ^~~
DistanceMatrix.c:1603:52: warning: ‘o’ may be used uninitialized [-Wmaybe-uninitialized]
1603 | if (o == 1) {
| ^
DistanceMatrix.c:1096:112: note: ‘o’ was declared here
1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^
DistanceMatrix.c:1606:91: warning: ‘ov’ may be used uninitialized [-Wmaybe-uninitialized]
1606 | sim[i] = (double)pos/((double)(ov + count + g2));
| ~~~^~~~~~~
DistanceMatrix.c:1096:88: note: ‘ov’ was declared here
1096 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^~
In function ‘distance’,
inlined from ‘distMatrix._omp_fn.0’ at DistanceMatrix.c:729:20:
DistanceMatrix.c:391:17: warning: ‘counts’ may be used uninitialized [-Wmaybe-uninitialized]
391 | free(counts);
| ^~~~~~~~~~~~
DistanceMatrix.c: In function ‘distMatrix._omp_fn.0’:
DistanceMatrix.c:137:30: note: ‘counts’ was declared here
137 | int i, j, I, J, m2, *counts;
| ^~~~~~
DistanceMatrix.c: In function ‘distMatrix’:
DistanceMatrix.c:624:33: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized]
624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads)
| ^~~
DistanceMatrix.c:545:13: note: ‘m’ was declared here
545 | int m, *lkup_row, *lkup_col;
| ^
DistanceMatrix.c:624:33: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized]
624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads)
| ^~~
DistanceMatrix.c:545:17: note: ‘lkup_row’ was declared here
545 | int m, *lkup_row, *lkup_col;
| ^~~~~~~~
DistanceMatrix.c:624:33: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized]
624 | #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads)
| ^~~
DistanceMatrix.c:545:28: note: ‘lkup_col’ was declared here
545 | int m, *lkup_row, *lkup_col;
| ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:546:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
546 | x = x + (x >> 4) & 0xF0F0F0F;
| ~~^~~~~~~~~~
EnumerateSequence.c: In function ‘enumerateSequence’:
EnumerateSequence.c:359:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized]
359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:318:14: note: ‘mN’ was declared here
318 | int *mN;
| ^~
EnumerateSequence.c:359:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:319:13: note: ‘tot’ was declared here
319 | int tot; // total number of k-mers
| ^~~
EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’:
EnumerateSequence.c:956:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized]
956 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:908:14: note: ‘mN’ was declared here
908 | int *mN;
| ^~
EnumerateSequence.c:956:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
956 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:909:13: note: ‘tot’ was declared here
909 | int tot; // total number of k-mers
| ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:464:43: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
464 | *rPercentComplete = floor(100*(double)(s + 1)/f_length);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:160:25: note: ‘rPercentComplete’ was declared here
160 | int before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
934 | #define eval Rf_eval
FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’
467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
FindFrameshifts.c:162:14: note: ‘percentComplete’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
934 | #define eval Rf_eval
FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’
467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
FindFrameshifts.c:317:34: warning: ‘I’ may be used uninitialized [-Wmaybe-uninitialized]
317 | while (i > 0 && j > 0) {
| ~~^~~
FindFrameshifts.c:135:28: note: ‘I’ was declared here
135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
| ^
FindFrameshifts.c:317:43: warning: ‘J’ may be used uninitialized [-Wmaybe-uninitialized]
317 | while (i > 0 && j > 0) {
| ~~^~~
FindFrameshifts.c:135:31: note: ‘J’ was declared here
135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
| ^
FindFrameshifts.c:376:28: warning: ‘K’ may be used uninitialized [-Wmaybe-uninitialized]
376 | if (k == 1) {
| ^
FindFrameshifts.c:135:34: note: ‘K’ was declared here
135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
| ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:422:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
422 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:389:22: note: ‘x_i.ptr’ was declared here
389 | Chars_holder x_i;
| ^~~
GeneFinding.c:432:57: warning: ‘lastVal’ may be used uninitialized [-Wmaybe-uninitialized]
432 | if (val < 64 && lastVal < 64)
| ~~~~~~~~^~~~
GeneFinding.c:372:32: note: ‘lastVal’ was declared here
372 | int i, j, s, fin, val, lastVal, dicodon;
| ^~~~~~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:798:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
798 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:772:22: note: ‘x_i.ptr’ was declared here
772 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:899:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
899 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:869:22: note: ‘x_i.ptr’ was declared here
869 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:952:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
952 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:929:22: note: ‘x_i.ptr’ was declared here
929 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1059 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1032:22: note: ‘x_i.ptr’ was declared here
1032 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1116:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1116 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1093:22: note: ‘x_i.ptr’ was declared here
1093 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1216 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1189:22: note: ‘x_i.ptr’ was declared here
1189 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1317:81: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1317 | seq[k] = getBaseLetterRC(x_i.ptr[j--]);
| ^
GeneFinding.c:1253:22: note: ‘x_i.ptr’ was declared here
1253 | Chars_holder x_i;
| ^~~
GeneFinding.c:1314:51: warning: ‘x_i.length’ may be used uninitialized [-Wmaybe-uninitialized]
1314 | (s == 0 && j >= 0 && j + w <= x_i.length)) {
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1253:22: note: ‘x_i.length’ was declared here
1253 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1379 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1351:22: note: ‘x_i.ptr’ was declared here
1351 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1496 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1462:22: note: ‘x_i.ptr’ was declared here
1462 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1598 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1574:22: note: ‘x_i.ptr’ was declared here
1574 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1712:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1712 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1682:22: note: ‘x_i.ptr’ was declared here
1682 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1827:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1827 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1789:22: note: ‘x_i.ptr’ was declared here
1789 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1914:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1914 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1883:22: note: ‘x_i.ptr’ was declared here
1883 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1993:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1993 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
| ^
GeneFinding.c:1951:22: note: ‘x_i.ptr’ was declared here
1951 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2093:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2093 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
| ^
GeneFinding.c:2058:22: note: ‘x_i.ptr’ was declared here
2058 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2308:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2308 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2277:22: note: ‘x_i.ptr’ was declared here
2277 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2426:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2426 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:2400:22: note: ‘x_i.ptr’ was declared here
2400 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2527:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2527 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:2497:22: note: ‘x_i.ptr’ was declared here
2497 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2578 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2555:22: note: ‘x_i.ptr’ was declared here
2555 | Chars_holder x_i;
| ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c GetPools.c -o GetPools.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Import.c -o Import.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c InformationContent.c -o InformationContent.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c IntDist.c -o IntDist.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ManipulateXStringSet.c -o ManipulateXStringSet.o
ManipulateXStringSet.c: In function ‘mergePairs._omp_fn.0’:
ManipulateXStringSet.c:1106:58: warning: ‘l2’ may be used uninitialized [-Wmaybe-uninitialized]
1106 | p2 = (l2 + pow(10, ((double)q2_i.ptr[s2 + 1] - 33)/-10))/2;
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ManipulateXStringSet.c:1087:36: note: ‘l2’ was declared here
1087 | double l1, l2; // last probability
| ^~
ManipulateXStringSet.c:1096:58: warning: ‘l1’ may be used uninitialized [-Wmaybe-uninitialized]
1096 | p1 = (l1 + pow(10, ((double)q1_i.ptr[s1 + 1] - 33)/-10))/2;
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ManipulateXStringSet.c:1087:32: note: ‘l1’ was declared here
1087 | double l1, l2; // last probability
| ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces]
79 | double dH[4][4] = {
| ^
80 | -7.9,-8.4,-7.8,-7.2
| {
81 | ,-8.5,-8.0,-10.6,-7.8
| }{
82 | ,-8.2,-9.8,-8.0,-8.4
| }{
83 | ,-7.2,-8.2,-8.5,-7.9
| }{
84 | };
| }
MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces]
88 | double dS[4][4] = {
| ^
89 | -22.2,-22.4,-21.0,-20.4
| {
90 | ,-22.7,-19.9,-27.2,-21.0
| }{
91 | ,-22.2,-24.4,-19.9,-22.4
| }{
92 | ,-21.3,-22.2,-22.7,-22.2
| }{
93 | };
| }
MeltPolymer.c:406:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized]
406 | SET_VECTOR_ELT(ret, s, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
MeltPolymer.c:53:19: note: ‘ans’ was declared here
53 | SEXP ret, ans;
| ^~~
MeltPolymer.c:358:41: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized]
358 | *(rans + k + l*s) += 1;
| ^~~~~~~~~~~~~~~~~
MeltPolymer.c:54:17: note: ‘rans’ was declared here
54 | double *rans;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c MovingAverage.c -o MovingAverage.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c NNLS.c -o NNLS.o
NNLS.c: In function ‘NNLS’:
NNLS.c:78:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
78 | *rPercentComplete = floor(100*((double)i + 1)/(double)l);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NNLS.c:40:34: note: ‘rPercentComplete’ was declared here
40 | int i, j, k, before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/include/Rdefines.h:41,
from NNLS.c:17:
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
934 | #define eval Rf_eval
NNLS.c:82:41: note: in expansion of macro ‘eval’
82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
NNLS.c:48:14: note: ‘percentComplete’ was declared here
48 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
934 | #define eval Rf_eval
NNLS.c:82:41: note: in expansion of macro ‘eval’
82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
NNLS.c:48:31: note: ‘utilsPackage’ was declared here
48 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Order.c -o Order.o
Order.c: In function ‘radixOrder’:
Order.c:169:41: warning: ‘bounds’ may be used uninitialized [-Wmaybe-uninitialized]
169 | #pragma omp parallel num_threads(NTHREADS)
| ^~~
Order.c:99:19: note: ‘bounds’ was declared here
99 | R_xlen_t *bounds;
| ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:446:39: warning: ‘p3’ may be used uninitialized [-Wmaybe-uninitialized]
446 | p3[0] = l1;
| ~~~~~~^~~~
PairwiseAlignment.c:176:24: note: ‘p3’ was declared here
176 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:447:39: warning: ‘p4’ may be used uninitialized [-Wmaybe-uninitialized]
447 | p4[0] = l2 - j1;
| ~~~~~~^~~~~~~~~
PairwiseAlignment.c:176:29: note: ‘p4’ was declared here
176 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:450:39: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized]
450 | p1[0] = l2;
| ~~~~~~^~~~
PairwiseAlignment.c:176:14: note: ‘p1’ was declared here
176 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:451:39: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized]
451 | p2[0] = l1 - i1;
| ~~~~~~^~~~~~~~~
PairwiseAlignment.c:176:19: note: ‘p2’ was declared here
176 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c: In function ‘alignPairs’:
PairwiseAlignment.c:1108:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
| ^~~
PairwiseAlignment.c:1036:25: note: ‘rPercentComplete’ was declared here
1036 | int before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
PairwiseAlignment.c:1108:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
| ^~~
PairwiseAlignment.c:1038:14: note: ‘percentComplete’ was declared here
1038 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
PairwiseAlignment.c:1108:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
| ^~~
PairwiseAlignment.c:1038:31: note: ‘utilsPackage’ was declared here
1038 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c PopulationGenetics.c -o PopulationGenetics.o
PopulationGenetics.c: In function ‘correlationProfile’:
PopulationGenetics.c:140:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
140 | *rPercentComplete = floor(100*soFar/tot);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
PopulationGenetics.c:40:68: note: ‘rPercentComplete’ was declared here
40 | int i, j, k, p, I, J, minL, warn = NA_INTEGER, v, before, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
PopulationGenetics.c:140:53: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
140 | *rPercentComplete = floor(100*soFar/tot);
| ^~~~~~~~~~~~~~~~~~~~
PopulationGenetics.c:41:31: note: ‘tot’ was declared here
41 | double weight, soFar, tot;
| ^~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/include/Rdefines.h:41,
from PopulationGenetics.c:11:
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
934 | #define eval Rf_eval
PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’
143 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
PopulationGenetics.c:50:14: note: ‘percentComplete’ was declared here
50 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
934 | #define eval Rf_eval
PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’
143 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
PopulationGenetics.c:50:31: note: ‘utilsPackage’ was declared here
50 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:601:25: warning: ‘leftSymbol’ may be used uninitialized [-Wmaybe-uninitialized]
601 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:489:14: note: ‘leftSymbol’ was declared here
489 | char leftSymbol, rightSymbol;
| ^~~~~~~~~~
PredictDBN.c:601:25: warning: ‘rightSymbol’ may be used uninitialized [-Wmaybe-uninitialized]
601 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:489:26: note: ‘rightSymbol’ was declared here
489 | char leftSymbol, rightSymbol;
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:51:31: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized]
51 | double HEC[N], temp, *rans;
| ^~~~
PredictHEC.c:247:43: warning: ‘states’ may be used uninitialized [-Wmaybe-uninitialized]
247 | states[j] = nms[0];
| ~~~~~~~~~~^~~~~~~~
PredictHEC.c:52:15: note: ‘states’ was declared here
52 | char *states;
| ^~~~~~
PredictHEC.c:273:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized]
273 | SET_VECTOR_ELT(ret, i, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:59:19: note: ‘ans’ was declared here
59 | SEXP ret, ans;
| ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Search.c -o Search.o
Search.c: In function ‘searchIndex._omp_fn.0’:
Search.c:578:92: warning: ‘subScores’ may be used uninitialized [-Wmaybe-uninitialized]
578 | if (lkup != NA_INTEGER && subScores[p1*l_i.length + lkup] != NA_REAL)
| ^
Search.c:317:33: note: ‘subScores’ was declared here
317 | double *subScores; // substitution scores (if maxIt > 0)
| ^~~~~~~~~
Search.c:449:66: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized]
449 | score2[j] = score[o1[j]];
| ^
Search.c:282:33: note: ‘score’ was declared here
282 | double *score, *addScore, *score2, *addScore2;
| ^~~~~
Search.c:450:72: warning: ‘addScore’ may be used uninitialized [-Wmaybe-uninitialized]
450 | addScore2[j] = addScore[o1[j]];
| ^
Search.c:282:41: note: ‘addScore’ was declared here
282 | double *score, *addScore, *score2, *addScore2;
| ^~~~~~~~
Search.c:587:83: warning: ‘maxLen’ may be used uninitialized [-Wmaybe-uninitialized]
587 | if (deltaTarget >= maxSep + maxLen) {
| ~~~~~~~^~~~~~~~
Search.c:560:45: note: ‘maxLen’ was declared here
560 | int maxLen; // maximum observed length
| ^~~~~~
Search.c:555:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
555 | Chars_holder p_i, s_j;
| ^~~
Search.c:626:55: warning: ‘s_j.length’ may be used uninitialized [-Wmaybe-uninitialized]
626 | bound = s_j.length - 1; // right bound
| ~~~~~~^~~~~~~~~~~~~~~~
Search.c:555:59: note: ‘s_j.length’ was declared here
555 | Chars_holder p_i, s_j;
| ^~~
Search.c:882:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
882 | Chars_holder p_i, s_j;
| ^~~
Search.c:1150:72: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized]
1150 | anchor[k++] = posQuery[p] + len[p] - 1;
| ^
Search.c:370:30: note: ‘len’ was declared here
370 | int *len; // length of each hit
| ^~~
Search.c:1139:58: warning: ‘chain’ may be used uninitialized [-Wmaybe-uninitialized]
1139 | while (p != chain[p]) {
| ^
Search.c:369:30: note: ‘chain’ was declared here
369 | int *chain; // set of joined hits per match
| ^~~~~
Search.c:371:30: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized]
371 | int *res; // indices of results
| ^~~
Search.c: In function ‘searchIndex’:
Search.c:224:17: warning: ‘sM’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:111:17: note: ‘sM’ was declared here
111 | double *sM, dS;
| ^~
Search.c:224:17: warning: ‘dS’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:111:21: note: ‘dS’ was declared here
111 | double *sM, dS;
| ^~
Search.c:224:17: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:112:14: note: ‘lkup_row’ was declared here
112 | int *lkup_row, *lkup_col, *pwv;
| ^~~~~~~~
Search.c:224:17: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:112:25: note: ‘lkup_col’ was declared here
112 | int *lkup_row, *lkup_col, *pwv;
| ^~~~~~~~
Search.c:224:17: warning: ‘pwv’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:112:36: note: ‘pwv’ was declared here
112 | int *lkup_row, *lkup_col, *pwv;
| ^~~
Search.c:224:17: warning: ‘scores’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:113:17: note: ‘scores’ was declared here
113 | double *scores, *addScores;
| ^~~~~~
Search.c:224:17: warning: ‘addScores’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:113:26: note: ‘addScores’ was declared here
113 | double *scores, *addScores;
| ^~~~~~~~~
Search.c:224:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:174:25: note: ‘rPercentComplete’ was declared here
174 | int before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
Search.c:224:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:176:14: note: ‘percentComplete’ was declared here
176 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
Search.c:224:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:176:31: note: ‘utilsPackage’ was declared here
176 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
Search.c:224:17: warning: ‘matrices’ may be used uninitialized [-Wmaybe-uninitialized]
224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:217:16: note: ‘matrices’ was declared here
217 | int ***matrices;
| ^~~~~~~~
Search.c:1287:38: warning: ‘anchors’ may be used uninitialized [-Wmaybe-uninitialized]
1287 | int *anchor = anchors[j];
| ^~~~~~
Search.c:1232:15: note: ‘anchors’ was declared here
1232 | int **anchors; // pointers to anchor positions
| ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Translate.c -o Translate.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Utils.c -o Utils.o
Utils.c: In function ‘splitPartitions’:
Utils.c:990:35: warning: ‘change’ may be used uninitialized [-Wmaybe-uninitialized]
990 | } else if (change - j >= m && // large enough partition
| ~~~~~~~^~~
Utils.c:984:13: note: ‘change’ was declared here
984 | int change; // index before start of partition
| ^~~~~~
Utils.c: In function ‘matchColumns’:
Utils.c:1198:55: warning: ‘lkup’ may be used uninitialized [-Wmaybe-uninitialized]
1198 | int val = lkup[(unsigned char)x_i.ptr[o[j]]];
| ^
Utils.c:1130:14: note: ‘lkup’ was declared here
1130 | int *lkup;
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c VectorSums.c -o VectorSums.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PopulationGenetics.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** 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 (DECIPHER)
DECIPHER.Rcheck/DECIPHER-Ex.timings
| name | user | system | elapsed | |
| AA_REDUCED | 0.042 | 0.009 | 0.051 | |
| Add2DB | 0.660 | 0.073 | 0.733 | |
| AdjustAlignment | 0.209 | 0.011 | 0.220 | |
| AlignDB | 1.506 | 0.099 | 1.608 | |
| AlignPairs | 4.899 | 0.149 | 5.053 | |
| AlignProfiles | 1.132 | 0.051 | 1.185 | |
| AlignSeqs | 193.127 | 1.203 | 194.340 | |
| AlignSynteny | 2.550 | 0.006 | 2.557 | |
| AlignTranslation | 11.516 | 0.092 | 11.609 | |
| AmplifyDNA | 0.002 | 0.002 | 0.004 | |
| Array2Matrix | 5.201 | 0.064 | 5.265 | |
| BLOSUM | 0.017 | 0.002 | 0.018 | |
| BrowseDB | 0.044 | 0.000 | 0.045 | |
| BrowseSeqs | 24.230 | 0.159 | 24.392 | |
| CalculateEfficiencyArray | 0.019 | 0.001 | 0.020 | |
| CalculateEfficiencyFISH | 0.004 | 0.001 | 0.004 | |
| CalculateEfficiencyPCR | 0.005 | 0.000 | 0.005 | |
| Clusterize | 8.304 | 0.063 | 8.368 | |
| Codec | 1.224 | 0.000 | 1.223 | |
| ConsensusSequence | 0.162 | 0.002 | 0.164 | |
| Cophenetic | 2.695 | 0.009 | 2.704 | |
| CorrectFrameshifts | 16.263 | 0.100 | 16.363 | |
| CreateChimeras | 0.658 | 0.001 | 0.659 | |
| DB2Seqs | 0.027 | 0.005 | 0.032 | |
| DesignArray | 5.225 | 0.035 | 5.261 | |
| DesignPrimers | 0.012 | 0.000 | 0.011 | |
| DesignProbes | 0.009 | 0.001 | 0.009 | |
| DesignSignatures | 0.007 | 0.003 | 0.010 | |
| DetectRepeats | 11.354 | 0.096 | 11.472 | |
| DigestDNA | 0.138 | 0.002 | 0.141 | |
| Disambiguate | 0.048 | 0.001 | 0.049 | |
| DistanceMatrix | 23.073 | 0.160 | 23.237 | |
| ExtractGenes | 38.961 | 0.642 | 39.608 | |
| FindChimeras | 0.086 | 0.001 | 0.086 | |
| FindGenes | 36.762 | 0.598 | 37.362 | |
| FindNonCoding | 60.997 | 0.613 | 61.615 | |
| FindSynteny | 1.617 | 0.019 | 1.636 | |
| FormGroups | 0.051 | 0.001 | 0.053 | |
| Genes-class | 35.859 | 0.264 | 36.124 | |
| HEC_MI | 0.261 | 0.003 | 0.264 | |
| IdConsensus | 0.417 | 0.009 | 0.426 | |
| IdLengths | 0.031 | 0.001 | 0.033 | |
| IdTaxa | 9.163 | 0.030 | 9.194 | |
| IdentifyByRank | 0.031 | 0.002 | 0.033 | |
| IndexSeqs | 0.949 | 0.000 | 0.949 | |
| InferDemography | 8.798 | 0.018 | 8.817 | |
| InferRecombination | 18.838 | 0.063 | 18.902 | |
| InferSelection | 38.109 | 0.095 | 38.206 | |
| InvertedIndex-class | 0.578 | 0.016 | 0.593 | |
| LearnNonCoding | 115.699 | 4.403 | 120.109 | |
| LearnTaxa | 6.268 | 0.643 | 6.911 | |
| MIQS | 0.042 | 0.003 | 0.044 | |
| MMLSUM | 0.008 | 0.001 | 0.009 | |
| MODELS | 0.002 | 0.000 | 0.002 | |
| MapCharacters | 3.791 | 0.016 | 3.808 | |
| MaskAlignment | 0.434 | 0.005 | 0.440 | |
| MeltDNA | 0.066 | 0.002 | 0.069 | |
| NNLS | 0.003 | 0.000 | 0.003 | |
| NonCoding-class | 0.058 | 0.004 | 0.061 | |
| NonCodingRNA | 0.111 | 0.005 | 0.116 | |
| OrientNucleotides | 0.454 | 0.002 | 0.456 | |
| PAM | 0.009 | 0.000 | 0.010 | |
| PFASUM | 0.009 | 0.001 | 0.011 | |
| PredictDBN | 0.006 | 0.002 | 0.008 | |
| PredictHEC | 0.294 | 0.002 | 0.296 | |
| RESTRICTION_ENZYMES | 0.001 | 0.004 | 0.004 | |
| ReadDendrogram | 0.021 | 0.001 | 0.022 | |
| RemoveGaps | 0.009 | 0.002 | 0.011 | |
| ScoreAlignment | 5.143 | 0.061 | 5.206 | |
| SearchDB | 0.077 | 0.013 | 0.091 | |
| SearchIndex | 1.245 | 0.011 | 1.257 | |
| Seqs2DB | 0.099 | 0.005 | 0.104 | |
| StaggerAlignment | 12.183 | 0.153 | 12.338 | |
| Synteny-class | 2.097 | 0.020 | 2.117 | |
| Taxa-class | 9.810 | 0.087 | 9.898 | |
| TerminalChar | 0.008 | 0.000 | 0.009 | |
| TileSeqs | 3.972 | 0.011 | 3.984 | |
| TrainingSet_16S | 2.083 | 0.005 | 2.087 | |
| Treeline | 59.380 | 0.296 | 59.679 | |
| TrimDNA | 9.765 | 0.124 | 9.891 | |
| WriteDendrogram | 0.004 | 0.000 | 0.004 | |
| WriteGenes | 33.245 | 0.451 | 33.698 | |
| deltaGrules | 0.007 | 0.004 | 0.011 | |
| deltaGrulesRNA | 0.023 | 0.002 | 0.024 | |
| deltaHrules | 0.019 | 0.001 | 0.021 | |
| deltaHrulesRNA | 0.019 | 0.001 | 0.020 | |
| deltaSrules | 0.050 | 0.002 | 0.052 | |
| deltaSrulesRNA | 0.018 | 0.000 | 0.017 | |