Erik Wright
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: devel |
| git_last_commit: 41542b7 |
| git_last_commit_date: 2024-02-25 07:36:27 -0400 (Sun, 25 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:37 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 517/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 2.31.3 (landing page) Erik Wright
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DECIPHER |
| Version: 2.31.3 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings DECIPHER_2.31.3.tar.gz |
| StartedAt: 2024-03-28 04:30:23 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:51:12 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 1248.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings DECIPHER_2.31.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.31.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 13.5Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.5Mb
extdata 2.3Mb
libs 1.9Mb
* 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 ... NOTE
checkRd: (-1) IdTaxa.Rd:27: Lost braces; missing escapes or markup?
27 | An object of class \code{Taxa} and subclass {Train} compatible with the class of \code{test}.
| ^
checkRd: (-1) IdTaxa.Rd:61: Lost braces; missing escapes or markup?
61 | If \code{type} is \code{"extended"} (the default) then an object of class \code{Taxa} and subclass {Train} is returned. This is stored as a list with elements corresponding to their respective sequence in \code{test}. Each list element contains components:
| ^
checkRd: (-1) LearnTaxa.Rd:75: Lost braces; missing escapes or markup?
75 | An object of class \code{Taxa} and subclass {Train}, which is stored as a list with components:
| ^
* 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 240.463 0.866 241.746
LearnNonCoding 140.568 1.665 142.464
MapCharacters 136.396 0.163 136.803
FindNonCoding 108.088 0.586 113.041
WriteGenes 51.532 0.103 51.731
ExtractGenes 49.990 0.252 50.342
Genes-class 49.344 0.064 49.497
FindGenes 46.428 0.064 46.585
BrowseSeqs 29.333 0.092 29.478
DetectRepeats 24.066 0.047 24.164
CorrectFrameshifts 20.850 0.056 20.950
StaggerAlignment 18.087 0.164 18.289
LearnTaxa 17.873 0.096 17.997
AlignTranslation 15.902 0.124 16.057
Taxa-class 13.808 0.040 13.879
TreeLine 13.252 0.072 13.357
IdTaxa 12.255 0.020 12.296
Clusterize 8.714 0.020 8.752
ScoreAlignment 7.052 0.028 7.096
TileSeqs 5.589 0.000 5.603
Array2Matrix 5.453 0.008 5.469
DesignArray 5.319 0.016 5.344
AlignPairs 4.972 0.112 5.098
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
DECIPHER.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL DECIPHER
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:426:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
426 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:39: note: ‘lGp’ was declared here
61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c:428:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
428 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:44: note: ‘lGs’ 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:1270:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1270 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:810:39: note: ‘lGp’ was declared here
810 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c:1272:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1272 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:810:44: note: ‘lGs’ was declared here
810 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:379:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
379 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads)
| ^~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:463:28: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
| ~~~~^~~~~
CalculateDeltaG.c:463:15: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
| ~~~~^~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:25:23: 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:31:23: 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:37:23: 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:43:23: 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:49:23: 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:55:23: 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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:524:28: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
524 | if (minX == minY && upX == upY) {
| ~~~~^~~~~~
ChainSegments.c:524:28: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:418:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
418 | minCs[i] = minC;
| ~~~~~~~~~^~~~~~
Cluster.c:246:50: 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:442:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
442 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:50: note: ‘minC’ was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:464:52: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
464 | rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
| ^
Cluster.c:781:13: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
781 | nDiv[j] -= dMatrix2[length*colIndices[j] - colIndices[j]*(colIndices[j] + 1)/2 + rowIndices[i] - colIndices[j]]; // col sums
| ^~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ClusterML.c -o ClusterML.o
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rdefines.h:38,
from ClusterML.c:16:
ClusterML.c: In function ‘clusterML’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/include/R_ext/RS.h:55:25: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
| ^~~~~~~~~~
ClusterML.c:1206:7: note: ‘Up’ was declared here
1206 | int *Up;
| ^~
ClusterML.c:1293:10: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
| ^~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:98:15: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
98 | int i, j, k, m, w;
| ^
ClusterMP.c:153:9: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized]
153 | int *P;
| ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:640:3: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
640 | free(Up);
| ^~~~~~~~
ClusterMP.c:140:10: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:140:10: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterMP.c:140:10: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:978:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
978 | p[c] = ((k - 1) >> 8) & 0xFF; // length of run
| ~~~^~~~
Compression.c:516:12: note: ‘k’ was declared here
516 | int i, j, k, pos;
| ^
Compression.c:1012:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1012 | count++;
| ~~~~~^~
Compression.c:544:29: note: ‘count’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~
Compression.c:1011:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1011 | word = (word << 8) | (unsigned int)reorder(byte);
| ~~~~~~^~~~~
Compression.c:544:23: note: ‘word’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1214:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1214 | p[c++] = rev == 0 ? 254 : 255;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
Compression.c:545:27: note: ‘rev’ was declared here
545 | int lastTemp, currTemp, rev, len, len2, thresh = 1;
| ^~~
Compression.c:558:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
558 | int lower = 0;
| ^~~~~
Compression.c:1241:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1241 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
| ~~~^~~~~~~~~~~~~~
Compression.c:631:12: note: ‘lastTriplet’ was declared here
631 | int run, lastTriplet, lastCase;
| ^~~~~~~~~~~
Compression.c:1031:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1031 | lastHit = dict[(word >> k) & 0xFF];
| ^
Compression.c:544:17: note: ‘dict’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfile’:
ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1578 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
455 | *(runs + s) += weight;
| ^~
ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here
397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
| ^~~~~~~
ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1771 | double *HEC, *s;
| ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:2046:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2046 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2046:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:1941:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1941 | int do_DBN, n, l, d;
| ^
ConsensusSequence.c:1940:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1940 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2189:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2189 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2189:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:2084:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2084 | int do_HEC, n, l, d;
| ^
ConsensusSequence.c:2083:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2083 | double *HEC, *s;
| ^~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:70:20: 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:77:20: 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:84:27: 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:838:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
838 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:37: note: ‘lastCycle’ was declared here
269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
DesignProbes.c:838:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
838 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:48: note: ‘thisCycle’ was declared here
269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:796:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
796 | if (!ci)
| ^~
DistanceMatrix.c:799:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
799 | while (i < ex) {
| ^~~~~
DistanceMatrix.c:818:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
818 | if (!cj)
| ^~
DistanceMatrix.c:821:4: 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:1053:11: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1053 | two != one) {
| ~~~~^~~~~~
DistanceMatrix.c:1028:8: note: ‘one’ was declared here
1028 | int one, two;
| ^~~
DistanceMatrix.c:1340:19: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1340 | if (w1 - p1 + p2 > w2 - t2) {
| ~~~~~~~~^~~~
DistanceMatrix.c:883:69: note: ‘p2’ 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:1340:14: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1340 | if (w1 - p1 + p2 > w2 - t2) {
| ~~~^~~~
DistanceMatrix.c:883:65: note: ‘p1’ 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:1374:31: warning: ‘off’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:883:89: 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:1374:31: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:883:85: 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:1379:42: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1379 | sim[i] = (double)pos/((double)(ov - g2));
| ~~~~^~~~~
DistanceMatrix.c:883:81: 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:1378:10: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1378 | if (o == 1) {
| ^
DistanceMatrix.c:883:105: 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;
| ^
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:459:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
459 | x = x + (x >> 4) & 0xF0F0F0F;
| ~~^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:381:14: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
381 | } else if (k == 2) {
| ^
FindFrameshifts.c:318:19: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
318 | if (C[k*rc + j*r + i] >= 0) {
| ~^~
FindFrameshifts.c:370:8: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
370 | i += B[k*rc + j*r + i];
| ~~^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rinternals.h:901:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
901 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rinternals.h:901:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
901 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
468 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:422:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
422 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:432:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
432 | score += codons[lastVal*64 + val];
| ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
791 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:892:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
892 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:973:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
973 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1059 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1131:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1131 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1216 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1286:23: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1286 | (s == 0 && j >= 0 && j + w <= x_i.length)) {
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1289:39: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1289 | seq[k] = getBaseLetterRC(x_i.ptr[j--]);
| ^
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1379 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1496 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1598 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1712:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1712 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1826:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1826 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1913:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1913 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1990:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1990 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2090:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2090 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2307:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2307 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2419:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2419 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2520:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2520 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2578 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:79:20: 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:88:20: 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:358:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
358 | *(rans + k + l*s) += 1;
| ^~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:472:11: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
472 | P2[i] = p2;
| ~~~~~~^~~~
PairwiseAlignment.c:175:12: note: ‘p2’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:471:11: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
471 | P1[i] = p1;
| ~~~~~~^~~~
PairwiseAlignment.c:175:7: note: ‘p1’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:476:11: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
476 | P4[i] = p4;
| ~~~~~~^~~~
PairwiseAlignment.c:175:22: note: ‘p4’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:475:11: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
475 | P3[i] = p3;
| ~~~~~~^~~~
PairwiseAlignment.c:175:17: note: ‘p3’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c: In function ‘alignPairs’:
PairwiseAlignment.c:1102:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1102 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
| ^~~
PairwiseAlignment.c:1102:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
PairwiseAlignment.c:1102:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:873:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
873 | range2[0] = nucs[pos[prev]];// + 1;
| ^
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:255:4: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
255 | SET_VECTOR_ELT(ret, i, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:233:16: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
233 | states[j] = 'C';
| ~~~~~~~~~~^~~~~
PredictHEC.c:237:18: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
237 | *(rans + 3*j + 1) = E;
| ~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:477:12: warning: ‘s_j.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
477 | bound = s_j.length - 1; // right bound
| ~~~~~~^~~~~~~~~~~~~~~~
Search.c:407:23: note: ‘s_j.length’ was declared here
407 | Chars_holder p_i, s_j;
| ^~~
Search.c:407:23: warning: ‘s_j.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c: In function ‘searchIndex’:
Search.c:839:5: warning: ‘ans3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
839 | SET_VECTOR_ELT(ans3, k, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
Search.c:166:9: warning: ‘matrices’ may be used uninitialized in this function [-Wmaybe-uninitialized]
166 | int ***matrices;
| ^~~~~~~~
Search.c:172:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
172 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
| ^~~
Search.c:172:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:172:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:172:10: warning: ‘lkup_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:172:10: warning: ‘lkup_row’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:172:10: warning: ‘dS’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:172:10: warning: ‘sM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Utils.c -o Utils.o
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rdefines.h:41,
from Utils.c:16:
Utils.c: In function ‘matchOrder’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rinternals.h:901:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
901 | #define eval Rf_eval
| ^~~~~~~
Utils.c:333:24: note: ‘utilsPackage’ was declared here
333 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rdefines.h:41,
from Utils.c:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rinternals.h:901:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
901 | #define eval Rf_eval
| ^~~~~~~
Utils.c:333:7: note: ‘percentComplete’ was declared here
333 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
Utils.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
431 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
Utils.c: In function ‘splitPartitions’:
Utils.c:1037:21: warning: ‘change’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1037 | } else if (change - j >= m && // large enough partition
| ~~~~~~~^~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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 | 0.060 | 0.004 | 0.064 | |
| Add2DB | 0.889 | 0.044 | 0.938 | |
| AdjustAlignment | 0.273 | 0.000 | 0.275 | |
| AlignDB | 1.961 | 0.064 | 2.033 | |
| AlignPairs | 4.972 | 0.112 | 5.098 | |
| AlignProfiles | 1.137 | 0.040 | 1.178 | |
| AlignSeqs | 240.463 | 0.866 | 241.746 | |
| AlignSynteny | 3.926 | 0.012 | 3.945 | |
| AlignTranslation | 15.902 | 0.124 | 16.057 | |
| AmplifyDNA | 0.002 | 0.000 | 0.003 | |
| Array2Matrix | 5.453 | 0.008 | 5.469 | |
| BrowseDB | 0.057 | 0.000 | 0.060 | |
| BrowseSeqs | 29.333 | 0.092 | 29.478 | |
| CalculateEfficiencyArray | 0.017 | 0.004 | 0.022 | |
| CalculateEfficiencyFISH | 0.006 | 0.000 | 0.007 | |
| CalculateEfficiencyPCR | 0.006 | 0.000 | 0.007 | |
| Clusterize | 8.714 | 0.020 | 8.752 | |
| Codec | 1.410 | 0.000 | 1.413 | |
| ConsensusSequence | 0.238 | 0.000 | 0.239 | |
| Cophenetic | 0.210 | 0.000 | 0.211 | |
| CorrectFrameshifts | 20.850 | 0.056 | 20.950 | |
| CreateChimeras | 1.037 | 0.004 | 1.043 | |
| DB2Seqs | 0.041 | 0.000 | 0.041 | |
| DesignArray | 5.319 | 0.016 | 5.344 | |
| DesignPrimers | 0.013 | 0.000 | 0.013 | |
| DesignProbes | 0.013 | 0.000 | 0.013 | |
| DesignSignatures | 0.014 | 0.000 | 0.014 | |
| DetectRepeats | 24.066 | 0.047 | 24.164 | |
| DigestDNA | 0.194 | 0.008 | 0.203 | |
| Disambiguate | 0.066 | 0.000 | 0.066 | |
| DistanceMatrix | 0.06 | 0.00 | 0.06 | |
| ExtractGenes | 49.990 | 0.252 | 50.342 | |
| FindChimeras | 0.094 | 0.004 | 0.099 | |
| FindGenes | 46.428 | 0.064 | 46.585 | |
| FindNonCoding | 108.088 | 0.586 | 113.041 | |
| FindSynteny | 2.273 | 0.011 | 2.288 | |
| FormGroups | 0.082 | 0.000 | 0.082 | |
| Genes-class | 49.344 | 0.064 | 49.497 | |
| HEC_MI | 0.205 | 0.004 | 0.209 | |
| IdConsensus | 0.565 | 0.012 | 0.577 | |
| IdLengths | 0.069 | 0.004 | 0.072 | |
| IdTaxa | 12.255 | 0.020 | 12.296 | |
| IdentifyByRank | 0.046 | 0.000 | 0.047 | |
| IndexSeqs | 0.995 | 0.000 | 0.997 | |
| InvertedIndex-class | 0.525 | 0.008 | 0.534 | |
| LearnNonCoding | 140.568 | 1.665 | 142.464 | |
| LearnTaxa | 17.873 | 0.096 | 17.997 | |
| MIQS | 0.039 | 0.004 | 0.043 | |
| MMLSUM | 0.009 | 0.000 | 0.009 | |
| MODELS | 0.002 | 0.000 | 0.002 | |
| MapCharacters | 136.396 | 0.163 | 136.803 | |
| MaskAlignment | 0.606 | 0.000 | 0.607 | |
| MeltDNA | 0.076 | 0.000 | 0.081 | |
| NNLS | 0.000 | 0.003 | 0.004 | |
| NonCoding-class | 0.053 | 0.003 | 0.056 | |
| NonCodingRNA | 0.101 | 0.000 | 0.101 | |
| OrientNucleotides | 0.537 | 0.004 | 0.542 | |
| PFASUM | 0.01 | 0.00 | 0.01 | |
| PredictDBN | 0.01 | 0.00 | 0.01 | |
| PredictHEC | 0.27 | 0.00 | 0.27 | |
| RESTRICTION_ENZYMES | 0.002 | 0.000 | 0.003 | |
| ReadDendrogram | 0.075 | 0.001 | 0.076 | |
| RemoveGaps | 0.014 | 0.002 | 0.017 | |
| ScoreAlignment | 7.052 | 0.028 | 7.096 | |
| SearchDB | 0.062 | 0.000 | 0.063 | |
| SearchIndex | 1.514 | 0.008 | 1.525 | |
| Seqs2DB | 0.141 | 0.004 | 0.146 | |
| StaggerAlignment | 18.087 | 0.164 | 18.289 | |
| Synteny-class | 3.100 | 0.008 | 3.116 | |
| Taxa-class | 13.808 | 0.040 | 13.879 | |
| TerminalChar | 0.008 | 0.000 | 0.009 | |
| TileSeqs | 5.589 | 0.000 | 5.603 | |
| TrainingSet_16S | 2.677 | 0.016 | 2.699 | |
| TreeLine | 13.252 | 0.072 | 13.357 | |
| TrimDNA | 0.169 | 0.004 | 0.173 | |
| WriteDendrogram | 0.001 | 0.004 | 0.004 | |
| WriteGenes | 51.532 | 0.103 | 51.731 | |
| deltaGrules | 0.011 | 0.000 | 0.010 | |
| deltaGrulesRNA | 0.021 | 0.000 | 0.021 | |
| deltaHrules | 0.018 | 0.000 | 0.018 | |
| deltaHrulesRNA | 0.017 | 0.000 | 0.017 | |
| deltaSrules | 0.073 | 0.004 | 0.077 | |
| deltaSrulesRNA | 0.013 | 0.003 | 0.015 | |