Erik Wright
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 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 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 507/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 3.1.4 (landing page) Erik Wright
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | 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: 3.1.4 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DECIPHER_3.1.4.tar.gz |
| StartedAt: 2024-07-15 23:18:13 -0400 (Mon, 15 Jul 2024) |
| EndedAt: 2024-07-15 23:34:04 -0400 (Mon, 15 Jul 2024) |
| EllapsedTime: 951.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DECIPHER_3.1.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 ... 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 whether package 'DECIPHER' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
installed size is 12.5Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.5Mb
extdata 2.5Mb
* 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 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 for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/DECIPHER/libs/x64/DECIPHER.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AlignSeqs 143.78 6.72 151.83
LearnNonCoding 78.30 7.62 86.22
WriteGenes 71.36 2.52 73.31
Genes-class 69.47 3.41 73.64
MapCharacters 67.84 0.50 68.55
ExtractGenes 65.74 2.50 68.18
FindGenes 64.72 2.52 67.31
FindNonCoding 51.95 12.02 66.57
BrowseSeqs 21.86 0.75 22.66
CorrectFrameshifts 12.14 0.69 12.86
StaggerAlignment 11.13 1.10 12.33
Taxa-class 10.33 0.35 10.70
DetectRepeats 9.72 0.64 10.44
AlignTranslation 8.59 0.60 9.32
IdTaxa 7.78 0.75 8.51
TreeLine 7.03 0.40 7.45
LearnTaxa 4.97 2.46 7.40
Array2Matrix 5.33 0.03 5.36
DesignArray 5.30 0.06 5.36
ScoreAlignment 5.00 0.22 5.25
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.
DECIPHER.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DECIPHER
###
##############################################################################
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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: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: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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
C:/Users/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;
| ^~~~~~~~~~~~~~~
C:/Users/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:795:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
795 | val = 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:896:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
896 | val = 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:2423:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
2423 | val = 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:2524:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
2524 | val = 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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
from NNLS.c:16:
C:/Users/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;
| ^~~~~~~~~~~~~~~
C:/Users/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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;
| ^~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:38,
from PredictDBN.c:16:
C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/RS.h:55:25: warning: 'MI' may be used uninitialized [-Wmaybe-uninitialized]
55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:1071:9: note: in expansion of macro 'Free'
1071 | Free(MI);
| ^~~~
PredictDBN.c:236:17: note: 'MI' was declared here
236 | double *MI = Calloc(tot*tot, double); // initialized to zero
| ^~
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictHEC.c -o PredictHEC.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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: 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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64
** 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
** 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 | 0.00 | 0.05 | 0.05 | |
| Add2DB | 0.53 | 0.13 | 0.65 | |
| AdjustAlignment | 0.16 | 0.01 | 0.17 | |
| AlignDB | 1.01 | 0.11 | 1.13 | |
| AlignPairs | 3.02 | 0.09 | 3.12 | |
| AlignProfiles | 1.16 | 0.08 | 1.23 | |
| AlignSeqs | 143.78 | 6.72 | 151.83 | |
| AlignSynteny | 2.31 | 0.03 | 2.35 | |
| AlignTranslation | 8.59 | 0.60 | 9.32 | |
| AmplifyDNA | 0 | 0 | 0 | |
| Array2Matrix | 5.33 | 0.03 | 5.36 | |
| BLOSUM | 0.02 | 0.00 | 0.02 | |
| BrowseDB | 0.03 | 0.02 | 0.04 | |
| BrowseSeqs | 21.86 | 0.75 | 22.66 | |
| CalculateEfficiencyArray | 0.00 | 0.01 | 0.02 | |
| CalculateEfficiencyFISH | 0 | 0 | 0 | |
| CalculateEfficiencyPCR | 0 | 0 | 0 | |
| Clusterize | 4.55 | 0.27 | 4.80 | |
| Codec | 1.27 | 0.00 | 1.26 | |
| ConsensusSequence | 0.14 | 0.00 | 0.14 | |
| Cophenetic | 0.12 | 0.00 | 0.13 | |
| CorrectFrameshifts | 12.14 | 0.69 | 12.86 | |
| CreateChimeras | 0.58 | 0.00 | 0.58 | |
| DB2Seqs | 0.01 | 0.00 | 0.03 | |
| DesignArray | 5.30 | 0.06 | 5.36 | |
| DesignPrimers | 0 | 0 | 0 | |
| DesignProbes | 0 | 0 | 0 | |
| DesignSignatures | 0.02 | 0.00 | 0.01 | |
| DetectRepeats | 9.72 | 0.64 | 10.44 | |
| DigestDNA | 0.11 | 0.00 | 0.11 | |
| Disambiguate | 0.05 | 0.00 | 0.04 | |
| DistanceMatrix | 0.03 | 0.00 | 0.03 | |
| ExtractGenes | 65.74 | 2.50 | 68.18 | |
| FindChimeras | 0.06 | 0.00 | 0.06 | |
| FindGenes | 64.72 | 2.52 | 67.31 | |
| FindNonCoding | 51.95 | 12.02 | 66.57 | |
| FindSynteny | 1.14 | 0.03 | 1.19 | |
| FormGroups | 0.03 | 0.03 | 0.06 | |
| Genes-class | 69.47 | 3.41 | 73.64 | |
| HEC_MI | 0.20 | 0.00 | 0.21 | |
| IdConsensus | 0.32 | 0.01 | 0.33 | |
| IdLengths | 0.03 | 0.00 | 0.03 | |
| IdTaxa | 7.78 | 0.75 | 8.51 | |
| IdentifyByRank | 0.03 | 0.02 | 0.05 | |
| IndexSeqs | 0.72 | 0.03 | 0.77 | |
| InvertedIndex-class | 0.45 | 0.00 | 0.45 | |
| LearnNonCoding | 78.30 | 7.62 | 86.22 | |
| LearnTaxa | 4.97 | 2.46 | 7.40 | |
| MIQS | 0.03 | 0.01 | 0.05 | |
| MMLSUM | 0.00 | 0.02 | 0.02 | |
| MODELS | 0 | 0 | 0 | |
| MapCharacters | 67.84 | 0.50 | 68.55 | |
| MaskAlignment | 0.39 | 0.08 | 0.47 | |
| MeltDNA | 0.06 | 0.00 | 0.06 | |
| NNLS | 0.02 | 0.00 | 0.02 | |
| NonCoding-class | 0.04 | 0.00 | 0.04 | |
| NonCodingRNA | 0.10 | 0.01 | 0.11 | |
| OrientNucleotides | 0.31 | 0.00 | 0.31 | |
| PAM | 0.00 | 0.02 | 0.02 | |
| PFASUM | 0.02 | 0.00 | 0.02 | |
| PredictDBN | 0.01 | 0.00 | 0.01 | |
| PredictHEC | 0.21 | 0.01 | 0.22 | |
| RESTRICTION_ENZYMES | 0 | 0 | 0 | |
| ReadDendrogram | 0.03 | 0.00 | 0.03 | |
| RemoveGaps | 0.01 | 0.00 | 0.02 | |
| ScoreAlignment | 5.00 | 0.22 | 5.25 | |
| SearchDB | 0.05 | 0.00 | 0.04 | |
| SearchIndex | 0.98 | 0.13 | 1.11 | |
| Seqs2DB | 0.14 | 0.01 | 0.16 | |
| StaggerAlignment | 11.13 | 1.10 | 12.33 | |
| Synteny-class | 1.53 | 0.01 | 1.58 | |
| Taxa-class | 10.33 | 0.35 | 10.70 | |
| TerminalChar | 0.00 | 0.01 | 0.01 | |
| TileSeqs | 2.97 | 0.02 | 2.99 | |
| TrainingSet_16S | 1.61 | 0.14 | 1.81 | |
| TreeLine | 7.03 | 0.40 | 7.45 | |
| TrimDNA | 1.06 | 0.00 | 1.08 | |
| WriteDendrogram | 0 | 0 | 0 | |
| WriteGenes | 71.36 | 2.52 | 73.31 | |
| deltaGrules | 0.02 | 0.00 | 0.02 | |
| deltaGrulesRNA | 0.01 | 0.01 | 0.03 | |
| deltaHrules | 0.02 | 0.00 | 0.01 | |
| deltaHrulesRNA | 0.00 | 0.03 | 0.03 | |
| deltaSrules | 0.01 | 0.02 | 0.08 | |
| deltaSrulesRNA | 0.00 | 0.03 | 0.03 | |