Erik Wright
| Snapshot Date: 2024-10-17 13:40 -0400 (Thu, 17 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: devel |
| git_last_commit: 6f007bb |
| git_last_commit_date: 2024-06-11 10:15:31 -0400 (Tue, 11 Jun 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-18 11:44 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
| 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 515/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 3.1.4 (landing page) Erik Wright
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 3.1.4 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DECIPHER_3.1.4.tar.gz |
| StartedAt: 2024-10-17 23:11:58 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 23:42:01 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 1802.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DECIPHER_3.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.1.4’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
installed size is 13.3Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.5Mb
extdata 2.5Mb
libs 1.4Mb
* 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 ‘.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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AlignSeqs 162.850 0.687 163.540
LearnNonCoding 113.747 4.380 118.131
MapCharacters 89.657 0.281 89.942
FindNonCoding 53.870 0.394 54.266
WriteGenes 44.345 0.195 44.548
ExtractGenes 41.755 0.325 42.082
Genes-class 41.780 0.072 41.853
FindGenes 41.384 0.188 41.576
BrowseSeqs 23.237 0.174 23.411
CorrectFrameshifts 15.449 0.040 15.489
StaggerAlignment 10.751 0.104 10.855
DetectRepeats 10.627 0.076 10.703
AlignTranslation 10.554 0.050 10.605
Taxa-class 10.009 0.043 10.052
IdTaxa 9.314 0.009 9.322
TreeLine 7.874 0.023 7.899
LearnTaxa 6.071 0.685 6.756
Clusterize 5.254 0.029 5.282
Array2Matrix 5.207 0.012 5.219
DesignArray 5.166 0.008 5.175
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
DECIPHER.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DECIPHER
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:437:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized]
437 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:51: note: ‘lGs’ was declared here
61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c:435:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized]
435 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:46: note: ‘lGp’ was declared here
61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1290:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized]
1290 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:819:51: note: ‘lGs’ was declared here
819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c:1288:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized]
1288 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:819:46: note: ‘lGp’ was declared here
819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:388:25: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized]
388 | #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:81:17: note: ‘subM’ was declared here
81 | double *subM;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:524:49: warning: ‘upY’ may be used uninitialized [-Wmaybe-uninitialized]
524 | if (minX == minY && upX == upY) {
| ~~~~^~~~~~
ChainSegments.c:490:93: note: ‘upY’ was declared here
490 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
| ^~~
ChainSegments.c:524:49: warning: ‘upX’ may be used uninitialized [-Wmaybe-uninitialized]
524 | if (minX == minY && upX == upY) {
| ~~~~^~~~~~
ChainSegments.c:490:88: note: ‘upX’ was declared here
490 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
| ^~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:418:50: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
418 | 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.1’:
Cluster.c:442:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
442 | 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:408:41: warning: ‘nDiv’ may be used uninitialized [-Wmaybe-uninitialized]
408 | #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:392:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
392 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterML.c -o ClusterML.o
ClusterML.c: In function ‘clusterML’:
ClusterML.c:1293:17: warning: ‘node’ may be used uninitialized [-Wmaybe-uninitialized]
1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
| ^~~
ClusterML.c:1170:17: note: ‘node’ was declared here
1170 | double *node;
| ^~~~
ClusterML.c:1293:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized]
1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
| ^~~
ClusterML.c:1206:14: note: ‘Up’ was declared here
1206 | int *Up;
| ^~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:165:41: warning: ‘P’ may be used uninitialized [-Wmaybe-uninitialized]
165 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:153:30: note: ‘P’ was declared here
153 | int *P;
| ^
ClusterMP.c:98:22: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized]
98 | int i, j, k, m, w;
| ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:140:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized]
140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:126:14: note: ‘Up’ was declared here
126 | int *Up;
| ^~
ClusterMP.c:140:17: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized]
140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:111:17: note: ‘lengths’ was declared here
111 | double *lengths, *score;
| ^~~~~~~
ClusterMP.c:140:17: warning: ‘nodes’ may be used uninitialized [-Wmaybe-uninitialized]
140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:112:14: note: ‘nodes’ was declared here
112 | int *nodes, *subM;
| ^~~~~
ClusterMP.c:140:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized]
140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:112:22: note: ‘subM’ was declared here
112 | int *nodes, *subM;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:1327:25: warning: ‘dict’ may be used uninitialized [-Wmaybe-uninitialized]
1327 | free(dict);
| ^~~~~~~~~~
Compression.c:544:31: note: ‘dict’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1241:71: warning: ‘lastTriplet’ may be used uninitialized [-Wmaybe-uninitialized]
1241 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
| ~~~^~~~~~~~~~~~~~
Compression.c:631:26: note: ‘lastTriplet’ was declared here
631 | int run, lastTriplet, lastCase;
| ^~~~~~~~~~~
Compression.c:1011:62: warning: ‘word’ may be used uninitialized [-Wmaybe-uninitialized]
1011 | word = (word << 8) | (unsigned int)reorder(byte);
| ~~~~~~^~~~~
Compression.c:544:37: note: ‘word’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1012:54: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized]
1012 | count++;
| ~~~~~^~
Compression.c:544:43: note: ‘count’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~
Compression.c:545:41: warning: ‘rev’ may be used uninitialized [-Wmaybe-uninitialized]
545 | int lastTemp, currTemp, rev, len, len2, thresh = 1;
| ^~~
Compression.c:1215:58: warning: ‘lastHit’ may be used uninitialized [-Wmaybe-uninitialized]
1215 | p[c++] = (unsigned char)lastHit;
| ^~~~~~~~~~~~~~~~~~~~~~
Compression.c:544:50: note: ‘lastHit’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:70:27: warning: missing braces around initializer [-Wmissing-braces]
70 | double NN[4][4] = {
| ^
71 | -0.816507461,-2.5401714,-1.647430026,-1.184658548
| {
72 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
| }{
73 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
| }{
74 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
| }{
75 | };
| }
DesignProbes.c:77:27: warning: missing braces around initializer [-Wmissing-braces]
77 | double PM[4][4] = {
| ^
78 | -0.141370102,-0.439805276,-0.285236035,-0.205111781
| {
79 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
| }{
80 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
| }{
81 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
| }{
82 | };
| }
DesignProbes.c:84:34: warning: missing braces around initializer [-Wmissing-braces]
84 | double sMM[4][5][5][4] = {
| ^
85 | 0,0,0,0
| {{{
86 | ,1.545032445,1.254355018,1.491691514,1.329138183
| }{
87 | ,1.150635633,0.582415494,1.075877275,1.187937642
| }{
88 | ,1.203555051,1.001540513,0.864287715,0.717125848
| }{
89 | ,0.75,0.65,0.69,0.78
| }{
90 | ,0.630005348,0.18553379,0.730763505,0.709272397
| -
| }},{{
91 | ,0,0,0,0
| }{
92 | ,0.856582783,-0.143236405,0.716721488,0.603652831
| }{
93 | ,0.851622883,0.653168672,0.676545316,1.187937642
| }{
94 | ,0.75,0.65,0.69,0.78
| }{
95 | ,1.231861002,0.746214538,1.087821916,0.989140748
| -
| }},{{
96 | ,1.822113278,1.270687029,1.336192565,1.364584949
| }{
97 | ,0,0,0,0
| }{
98 | ,1.443665704,1.385046493,1.256013166,1.329138183
| }{
99 | ,0.75,0.65,0.69,0.78
| }{
100 | ,1.478009492,0.882097231,1.20450984,1.061002478
| -
| }},{{
101 | ,1.496720812,0.846496194,0.967868114,0.989140748
| }{
102 | ,0.766581547,-0.024857805,0.50754303,0.709272397
| }{
103 | ,0,0,0,0
| }{
104 | ,0.75,0.65,0.69,0.78
| }{
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 | ,0.76,0.65,0.69,0.78
| }{
109 | ,0,0,0,0
| }{
110 | ,0,0,0,0
| -
| }}},{{{
111 | ,1.295827995,0.84547091,0.91019099,1.256013166
| }{
112 | ,0.755889609,0.241428373,0.396379912,0.676545316
| }{
113 | ,0.99945386,0.740323132,0.435659206,0.864287715
| }{
114 | ,0.65,0.55,0.48,0.69
| }{
115 | ,0.843147406,0.101248351,0.49063599,0.50754303
| -
| }},{{
116 | ,0,0,0,0
| }{
117 | ,1.0651638,0.249934344,0.699352949,0.716721488
| }{
118 | ,0.871921533,0.59458138,0.396379912,1.075877275
| }{
119 | ,0.65,0.56,0.49,0.69
| }{
120 | ,1.07531714,0.318907854,0.653287717,0.967868114
| -
| }},{{
121 | ,1.099899195,0.730184613,0.661798984,1.336192565
| }{
122 | ,0,0,0,0
| }{
123 | ,1.45897431,1.318532145,0.91019099,1.491691514
| }{
124 | ,0.65,0.56,0.49,0.69
| }{
125 | ,1.242135174,0.894838095,1.108555445,1.20450984
| -
| }},{{
126 | ,0.911428974,0.524430101,0.653287717,1.087821916
| }{
127 | ,0.503209827,0.274849491,0.49063599,0.730763505
| }{
128 | ,0,0,0,0
| }{
129 | ,0.65,0.55,0.48,0.69
| }{
130 | ,0.65,0.55,0.48,0.69
| -
| }},{{
131 | ,0.65,0.56,0.49,0.69
| }{
132 | ,0.65,0.56,0.49,0.69
| }{
133 | ,0.65,0.55,0.48,0.69
| }{
134 | ,0,0,0,0
| }{
135 | ,0,0,0,0
| -
| }}},{{{
136 | ,1.100661785,0.969784756,1.318532145,1.385046493
| }{
137 | ,0.565895968,-0.060347902,0.59458138,0.653168672
| }{
138 | ,0.782168488,0.788161238,0.740323132,1.001540513
| }{
139 | ,0.68,0.46,0.55,0.65
| }{
140 | ,0.468913405,-0.469855984,0.274849491,-0.024857805
| -
| }},{{
141 | ,0,0,0,0
| }{
142 | ,0.258195131,-0.70438632,0.249934344,-0.143236405
| }{
143 | ,0.502914193,-0.060347902,0.241428373,0.582415494
| }{
144 | ,0.68,0.47,0.56,0.65
| }{
145 | ,0.584083861,0.258975454,0.524430101,0.846496194
| -
| }},{{
146 | ,0.968040559,0.797499702,0.730184613,1.270687029
| }{
147 | ,0,0,0,0
| }{
148 | ,1.081040749,0.969784756,0.84547091,1.254355018
| }{
149 | ,0.68,0.47,0.56,0.65
| }{
150 | ,1.048553951,0.728354541,0.894838095,0.882097231
| -
| }},{{
151 | ,0.88611252,0.258975454,0.318907854,0.746214538
| }{
152 | ,0.239520858,-0.469855984,0.101248351,0.18553379
| }{
153 | ,0,0,0,0
| }{
154 | ,0.68,0.46,0.55,0.65
| }{
155 | ,0.68,0.46,0.55,0.65
| -
| }},{{
156 | ,0.68,0.47,0.56,0.65
| }{
157 | ,0.68,0.47,0.56,0.65
| }{
158 | ,0.68,0.46,0.55,0.65
| }{
159 | ,0,0,0,0
| }{
160 | ,0,0,0,0
| -
| }}},{{{
161 | ,1.566899704,1.081040749,1.45897431,1.443665704
| }{
162 | ,0.976725675,0.502914193,0.871921533,0.851622883
| }{
163 | ,1.482046826,0.782168488,0.99945386,1.203555051
| }{
164 | ,0.85,0.68,0.65,0.76
| }{
165 | ,0.798628781,0.239520858,0.503209827,0.766581547
| -
| }},{{
166 | ,0,0,0,0
| }{
167 | ,1.141098246,0.258195131,1.0651638,0.856582783
| }{
168 | ,0.976725675,0.565895968,0.755889609,1.150635633
| }{
169 | ,0.85,0.68,0.65,0.75
| }{
170 | ,1.125403302,0.88611252,0.911428974,1.496720812
| -
| }},{{
171 | ,1.68169282,0.968040559,1.099899195,1.822113278
| }{
172 | ,0,0,0,0
| }{
173 | ,1.566899704,1.100661785,1.295827995,1.545032445
| }{
174 | ,0.85,0.68,0.65,0.75
| }{
175 | ,1.35948517,1.048553951,1.242135174,1.478009492
| -
| }},{{
176 | ,1.125403302,0.584083861,1.07531714,1.231861002
| }{
177 | ,0.798628781,0.468913405,0.843147406,0.630005348
| }{
178 | ,0,0,0,0
| }{
179 | ,0.85,0.68,0.65,0.75
| }{
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 | ,0,0,0,0
| }{
185 | };
| }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:837:60: warning: ‘lastCycle’ may be used uninitialized [-Wmaybe-uninitialized]
837 | if (thisCycle < lastCycle) {
| ^
DesignProbes.c:269:58: note: ‘lastCycle’ was declared here
269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
DesignProbes.c:837:60: warning: ‘thisCycle’ may be used uninitialized [-Wmaybe-uninitialized]
837 | if (thisCycle < lastCycle) {
| ^
DesignProbes.c:269:69: note: ‘thisCycle’ was declared here
269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:796:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
796 | if (!ci)
| ^~
DistanceMatrix.c:799:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
799 | while (i < ex) {
| ^~~~~
DistanceMatrix.c:818:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
818 | if (!cj)
| ^~
DistanceMatrix.c:821:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
821 | while (j < ey) {
| ^~~~~
DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’:
DistanceMatrix.c:1374:66: warning: ‘OV’ may be used uninitialized [-Wmaybe-uninitialized]
1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:883:92: note: ‘OV’ was declared here
883 | 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:1374:66: warning: ‘off’ may be used uninitialized [-Wmaybe-uninitialized]
1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:883:96: note: ‘off’ was declared here
883 | 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:1053:53: warning: ‘one’ may be used uninitialized [-Wmaybe-uninitialized]
1053 | two != one) {
| ~~~~^~~~~~
DistanceMatrix.c:1028:29: note: ‘one’ was declared here
1028 | int one, two;
| ^~~
DistanceMatrix.c:1390:52: warning: ‘o’ may be used uninitialized [-Wmaybe-uninitialized]
1390 | if (o == 1) {
| ^
DistanceMatrix.c:883:112: note: ‘o’ was declared here
883 | 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:1393:91: warning: ‘ov’ may be used uninitialized [-Wmaybe-uninitialized]
1393 | sim[i] = (double)pos/((double)(ov + count + g2));
| ~~~^~~~~~~
DistanceMatrix.c:883:88: note: ‘ov’ was declared here
883 | 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;
| ^~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:545:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
545 | x = x + (x >> 4) & 0xF0F0F0F;
| ~~^~~~~~~~~~
EnumerateSequence.c: In function ‘enumerateSequence’:
EnumerateSequence.c:358:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized]
358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:317:14: note: ‘mN’ was declared here
317 | int *mN;
| ^~
EnumerateSequence.c:358:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:318:13: note: ‘tot’ was declared here
318 | int tot; // total number of k-mers
| ^~~
EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’:
EnumerateSequence.c:955:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized]
955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:907:14: note: ‘mN’ was declared here
907 | int *mN;
| ^~
EnumerateSequence.c:955:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
| ^~~
EnumerateSequence.c:908:13: note: ‘tot’ was declared here
908 | int tot; // total number of k-mers
| ^~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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-3.20-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:903:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
903 | #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-3.20-bioc/R/include/Rinternals.h:903:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
903 | #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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:421:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
421 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:388:22: note: ‘x_i.ptr’ was declared here
388 | Chars_holder x_i;
| ^~~
GeneFinding.c:431:57: warning: ‘lastVal’ may be used uninitialized [-Wmaybe-uninitialized]
431 | if (val < 64 && lastVal < 64)
| ~~~~~~~~^~~~
GeneFinding.c:371:32: note: ‘lastVal’ was declared here
371 | int i, j, s, fin, val, lastVal, dicodon;
| ^~~~~~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:797:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
797 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:771:22: note: ‘x_i.ptr’ was declared here
771 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:898:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
898 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:868:22: note: ‘x_i.ptr’ was declared here
868 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:951:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
951 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:928:22: note: ‘x_i.ptr’ was declared here
928 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1058:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1058 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1031:22: note: ‘x_i.ptr’ was declared here
1031 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1115:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1115 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1092:22: note: ‘x_i.ptr’ was declared here
1092 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1215:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1215 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1188:22: note: ‘x_i.ptr’ was declared here
1188 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1316:81: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1316 | seq[k] = getBaseLetterRC(x_i.ptr[j--]);
| ^
GeneFinding.c:1252:22: note: ‘x_i.ptr’ was declared here
1252 | Chars_holder x_i;
| ^~~
GeneFinding.c:1313:51: warning: ‘x_i.length’ may be used uninitialized [-Wmaybe-uninitialized]
1313 | (s == 0 && j >= 0 && j + w <= x_i.length)) {
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:22: note: ‘x_i.length’ was declared here
1252 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1378:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1378 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1350:22: note: ‘x_i.ptr’ was declared here
1350 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1495:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1495 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1461:22: note: ‘x_i.ptr’ was declared here
1461 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1597:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1597 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1573:22: note: ‘x_i.ptr’ was declared here
1573 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1711:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1711 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1681:22: note: ‘x_i.ptr’ was declared here
1681 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1826:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1826 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1788:22: note: ‘x_i.ptr’ was declared here
1788 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1913:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1913 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1882:22: note: ‘x_i.ptr’ was declared here
1882 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1992:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
1992 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
| ^
GeneFinding.c:1950:22: note: ‘x_i.ptr’ was declared here
1950 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2092:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2092 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
| ^
GeneFinding.c:2057:22: note: ‘x_i.ptr’ was declared here
2057 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2307:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2307 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2276:22: note: ‘x_i.ptr’ was declared here
2276 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2425:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2425 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:2399:22: note: ‘x_i.ptr’ was declared here
2399 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2526:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2526 | val += 16*getBase(x_i.ptr[j]);
| ^
GeneFinding.c:2496:22: note: ‘x_i.ptr’ was declared here
2496 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2577:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
2577 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2554:22: note: ‘x_i.ptr’ was declared here
2554 | Chars_holder x_i;
| ^~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NNLS.c -o NNLS.o
NNLS.c: In function ‘NNLS’:
NNLS.c:77:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
77 | *rPercentComplete = floor(100*((double)i + 1)/(double)l);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NNLS.c:39:34: note: ‘rPercentComplete’ was declared here
39 | int i, j, k, before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
from NNLS.c:16:
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:903:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
903 | #define eval Rf_eval
NNLS.c:81:41: note: in expansion of macro ‘eval’
81 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
NNLS.c:47:14: note: ‘percentComplete’ was declared here
47 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:903:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
903 | #define eval Rf_eval
NNLS.c:81:41: note: in expansion of macro ‘eval’
81 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
| ^~~~
NNLS.c:47:31: note: ‘utilsPackage’ was declared here
47 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:445:39: warning: ‘p3’ may be used uninitialized [-Wmaybe-uninitialized]
445 | p3[0] = l1;
| ~~~~~~^~~~
PairwiseAlignment.c:175:24: note: ‘p3’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:446:39: warning: ‘p4’ may be used uninitialized [-Wmaybe-uninitialized]
446 | p4[0] = l2 - j1;
| ~~~~~~^~~~~~~~~
PairwiseAlignment.c:175:29: note: ‘p4’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:449:39: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized]
449 | p1[0] = l2;
| ~~~~~~^~~~
PairwiseAlignment.c:175:14: note: ‘p1’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:450:39: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized]
450 | p2[0] = l1 - i1;
| ~~~~~~^~~~~~~~~
PairwiseAlignment.c:175:19: note: ‘p2’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c: In function ‘alignPairs’:
PairwiseAlignment.c:1107:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
| ^~~
PairwiseAlignment.c:1035:25: note: ‘rPercentComplete’ was declared here
1035 | int before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
PairwiseAlignment.c:1107:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
| ^~~
PairwiseAlignment.c:1037:14: note: ‘percentComplete’ was declared here
1037 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
PairwiseAlignment.c:1107:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
| ^~~
PairwiseAlignment.c:1037:31: note: ‘utilsPackage’ was declared here
1037 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:597:25: warning: ‘leftSymbol’ may be used uninitialized [-Wmaybe-uninitialized]
597 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:485:14: note: ‘leftSymbol’ was declared here
485 | char leftSymbol, rightSymbol;
| ^~~~~~~~~~
PredictDBN.c:597:25: warning: ‘rightSymbol’ may be used uninitialized [-Wmaybe-uninitialized]
597 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:485:26: note: ‘rightSymbol’ was declared here
485 | char leftSymbol, rightSymbol;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Search.c -o Search.o
Search.c: In function ‘searchIndex._omp_fn.0’:
Search.c:475:75: warning: ‘maxLen’ may be used uninitialized [-Wmaybe-uninitialized]
475 | if (deltaTarget >= maxSep + maxLen) {
| ~~~~~~~^~~~~~~~
Search.c:449:37: note: ‘maxLen’ was declared here
449 | int maxLen; // maximum observed length
| ^~~~~~
Search.c:443:51: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
443 | Chars_holder p_i, s_j;
| ^~~
Search.c:515:47: warning: ‘s_j.length’ may be used uninitialized [-Wmaybe-uninitialized]
515 | bound = s_j.length - 1; // right bound
| ~~~~~~^~~~~~~~~~~~~~~~
Search.c:443:51: note: ‘s_j.length’ was declared here
443 | Chars_holder p_i, s_j;
| ^~~
Search.c: In function ‘searchIndex’:
Search.c:208:17: warning: ‘sM’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:104:17: note: ‘sM’ was declared here
104 | double *sM, dS;
| ^~
Search.c:208:17: warning: ‘dS’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:104:21: note: ‘dS’ was declared here
104 | double *sM, dS;
| ^~
Search.c:208:17: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:105:14: note: ‘lkup_row’ was declared here
105 | int *lkup_row, *lkup_col;
| ^~~~~~~~
Search.c:208:17: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:105:25: note: ‘lkup_col’ was declared here
105 | int *lkup_row, *lkup_col;
| ^~~~~~~~
Search.c:208:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:133:25: note: ‘rPercentComplete’ was declared here
133 | int before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
Search.c:208:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:135:14: note: ‘percentComplete’ was declared here
135 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
Search.c:208:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:135:31: note: ‘utilsPackage’ was declared here
135 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
Search.c:208:17: warning: ‘matrices’ may be used uninitialized [-Wmaybe-uninitialized]
208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:201:16: note: ‘matrices’ was declared here
201 | int ***matrices;
| ^~~~~~~~
Search.c:943:38: warning: ‘anchors’ may be used uninitialized [-Wmaybe-uninitialized]
943 | int *anchor = anchors[j];
| ^~~~~~
Search.c:888:15: note: ‘anchors’ was declared here
888 | int **anchors; // pointers to anchor positions
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Utils.c -o Utils.o
Utils.c: In function ‘splitPartitions’:
Utils.c:982:35: warning: ‘change’ may be used uninitialized [-Wmaybe-uninitialized]
982 | } else if (change - j >= m && // large enough partition
| ~~~~~~~^~~
Utils.c:976:13: note: ‘change’ was declared here
976 | int change; // index before start of partition
| ^~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.20-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 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 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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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 | 0.036 | 0.003 | 0.039 | |
| Add2DB | 0.566 | 0.063 | 0.630 | |
| AdjustAlignment | 0.188 | 0.003 | 0.192 | |
| AlignDB | 1.151 | 0.039 | 1.192 | |
| AlignPairs | 3.857 | 0.061 | 3.919 | |
| AlignProfiles | 0.953 | 0.007 | 0.959 | |
| AlignSeqs | 162.850 | 0.687 | 163.540 | |
| AlignSynteny | 2.500 | 0.004 | 2.504 | |
| AlignTranslation | 10.554 | 0.050 | 10.605 | |
| AmplifyDNA | 0.002 | 0.000 | 0.002 | |
| Array2Matrix | 5.207 | 0.012 | 5.219 | |
| BLOSUM | 0.018 | 0.000 | 0.018 | |
| BrowseDB | 0.034 | 0.000 | 0.035 | |
| BrowseSeqs | 23.237 | 0.174 | 23.411 | |
| CalculateEfficiencyArray | 0.018 | 0.001 | 0.019 | |
| CalculateEfficiencyFISH | 0.003 | 0.001 | 0.004 | |
| CalculateEfficiencyPCR | 0.004 | 0.000 | 0.003 | |
| Clusterize | 5.254 | 0.029 | 5.282 | |
| Codec | 1.005 | 0.000 | 1.004 | |
| ConsensusSequence | 0.145 | 0.003 | 0.148 | |
| Cophenetic | 0.179 | 0.000 | 0.180 | |
| CorrectFrameshifts | 15.449 | 0.040 | 15.489 | |
| CreateChimeras | 0.625 | 0.001 | 0.626 | |
| DB2Seqs | 0.025 | 0.004 | 0.027 | |
| DesignArray | 5.166 | 0.008 | 5.175 | |
| DesignPrimers | 0.008 | 0.000 | 0.008 | |
| DesignProbes | 0.006 | 0.000 | 0.007 | |
| DesignSignatures | 0.007 | 0.000 | 0.007 | |
| DetectRepeats | 10.627 | 0.076 | 10.703 | |
| DigestDNA | 0.123 | 0.002 | 0.126 | |
| Disambiguate | 0.04 | 0.00 | 0.04 | |
| DistanceMatrix | 0.034 | 0.001 | 0.035 | |
| ExtractGenes | 41.755 | 0.325 | 42.082 | |
| FindChimeras | 0.059 | 0.000 | 0.059 | |
| FindGenes | 41.384 | 0.188 | 41.576 | |
| FindNonCoding | 53.870 | 0.394 | 54.266 | |
| FindSynteny | 1.250 | 0.001 | 1.251 | |
| FormGroups | 0.044 | 0.001 | 0.045 | |
| Genes-class | 41.780 | 0.072 | 41.853 | |
| HEC_MI | 0.257 | 0.001 | 0.258 | |
| IdConsensus | 0.336 | 0.007 | 0.343 | |
| IdLengths | 0.028 | 0.001 | 0.029 | |
| IdTaxa | 9.314 | 0.009 | 9.322 | |
| IdentifyByRank | 0.027 | 0.000 | 0.027 | |
| IndexSeqs | 0.862 | 0.002 | 0.863 | |
| InvertedIndex-class | 0.482 | 0.000 | 0.482 | |
| LearnNonCoding | 113.747 | 4.380 | 118.131 | |
| LearnTaxa | 6.071 | 0.685 | 6.756 | |
| MIQS | 0.040 | 0.005 | 0.045 | |
| MMLSUM | 0.008 | 0.001 | 0.009 | |
| MODELS | 0.000 | 0.001 | 0.001 | |
| MapCharacters | 89.657 | 0.281 | 89.942 | |
| MaskAlignment | 0.356 | 0.004 | 0.359 | |
| MeltDNA | 0.063 | 0.003 | 0.065 | |
| NNLS | 0.001 | 0.002 | 0.002 | |
| NonCoding-class | 0.131 | 0.003 | 0.134 | |
| NonCodingRNA | 0.111 | 0.001 | 0.112 | |
| OrientNucleotides | 0.412 | 0.001 | 0.413 | |
| PAM | 0.008 | 0.001 | 0.008 | |
| PFASUM | 0.01 | 0.00 | 0.01 | |
| PredictDBN | 0.006 | 0.001 | 0.007 | |
| PredictHEC | 0.267 | 0.004 | 0.270 | |
| RESTRICTION_ENZYMES | 0.001 | 0.001 | 0.002 | |
| ReadDendrogram | 0.020 | 0.000 | 0.021 | |
| RemoveGaps | 0.01 | 0.00 | 0.01 | |
| ScoreAlignment | 4.416 | 0.025 | 4.441 | |
| SearchDB | 0.044 | 0.000 | 0.044 | |
| SearchIndex | 0.937 | 0.025 | 0.962 | |
| Seqs2DB | 0.102 | 0.004 | 0.106 | |
| StaggerAlignment | 10.751 | 0.104 | 10.855 | |
| Synteny-class | 1.675 | 0.005 | 1.680 | |
| Taxa-class | 10.009 | 0.043 | 10.052 | |
| TerminalChar | 0.006 | 0.000 | 0.006 | |
| TileSeqs | 2.922 | 0.000 | 2.922 | |
| TrainingSet_16S | 1.634 | 0.004 | 1.638 | |
| TreeLine | 7.874 | 0.023 | 7.899 | |
| TrimDNA | 0.103 | 0.000 | 0.103 | |
| WriteDendrogram | 0.003 | 0.000 | 0.003 | |
| WriteGenes | 44.345 | 0.195 | 44.548 | |
| deltaGrules | 0.009 | 0.000 | 0.009 | |
| deltaGrulesRNA | 0.021 | 0.000 | 0.022 | |
| deltaHrules | 0.017 | 0.001 | 0.018 | |
| deltaHrulesRNA | 0.017 | 0.000 | 0.017 | |
| deltaSrules | 0.046 | 0.001 | 0.047 | |
| deltaSrulesRNA | 0.014 | 0.001 | 0.016 | |