Hi,
don't know much about it, but at least to a certain extent your errors
might be connected to this
<https://developer.r-project.org/blosxom.cgi/R-devel/2024/11/11>.
Best,
Oleksii
On Tue, 10 Dec 2024 at 22:32, Tulip Nandu <tulip.na...@utsouthwestern.edu>
wrote:
> Hi,
> I solved the error of decideTests() but now there is a whole bunch of
> compilation error. Can anyone please guide me through this?
>
>
>
> ############################################################################
>
> ##############################################################################
> ###
> ### Running command:
> ###
> ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs
> --no-resave-data groHMM
> ###
>
> ##############################################################################
>
> ##############################################################################
>
>
> * checking for file ‘groHMM/DESCRIPTION’ ... OK
> * preparing ‘groHMM’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> -----------------------------------
> * installing *source* package ‘groHMM’ ...
> ** using staged installation
> ** libs
> using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> AnnotateProbes.c -o AnnotateProbes.o
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> DecayAlgorithm.c -o DecayAlgorithm.o
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> MLEfit.c -o MLEfit.o
> In file included from MLEfit.c:43:
> hmmHeader.h:301:16: warning: ‘expSum’ defined but not used
> [-Wunused-function]
> 301 | static double expSum(double *logValues, int length) {
> | ^~~~~~
> hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not
> used [-Wunused-function]
> 281 | static double MargainalizeSumLogProbOver(int state, int position,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> RegisterRRoutines.c -o RegisterRRoutines.o
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> Windowing.c -o Windowing.o
> Windowing.c: In function ‘WindowAnalysis’:
> Windowing.c:146:13: warning: unused variable ‘II’ [-Wunused-variable]
> 146 | int II = 0;
> | ^~
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> hmmEM.c -o hmmEM.o
> In file included from hmmEM.c:50:
> hmmHeader.h:301:16: warning: ‘expSum’ defined but not used
> [-Wunused-function]
> 301 | static double expSum(double *logValues, int length) {
> | ^~~~~~
> hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not
> used [-Wunused-function]
> 281 | static double MargainalizeSumLogProbOver(int state, int position,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from hmmHeader.h:36:
> UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not
> used [-Wunused-variable]
> 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
> | ^~~~~~~~~~~~~~~~~~~~~~~
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> hmmFwBw.c -o hmmFwBw.o
> hmmFwBw.c: In function ‘forward’:
> hmmFwBw.c:142:7: warning: this ‘for’ clause does not guard...
> [-Wmisleading-indentation]
> 142 | for(k=1; k<n; k++)
> | ^~~
> hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly
> indented as if it were guarded by the ‘for’
> 145 | for (k = 0; k<n; k++) {
> | ^~~
> In file included from hmmFwBw.c:45:
> hmmHeader.h: At top level:
> hmmHeader.h:301:16: warning: ‘expSum’ defined but not used
> [-Wunused-function]
> 301 | static double expSum(double *logValues, int length) {
> | ^~~~~~
> hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not
> used [-Wunused-function]
> 281 | static double MargainalizeSumLogProbOver(int state, int position,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from hmmHeader.h:36:
> UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not
> used [-Wunused-variable]
> 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
> | ^~~~~~~~~~~~~~~~~~~~~~~
> gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG
> -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c
> hmmMiscFunctions.c -o hmmMiscFunctions.o
> hmmMiscFunctions.c: In function ‘SStatsGamma’:
> hmmMiscFunctions.c:235:37: warning: format ‘%d’ expects argument of type
> ‘int’, but argument 2 has type ‘double’ [-Wformat=]
> 235 | if(!(logPP <= epsilon)) Rprintf("[SSallocGamma] -- \
> | ^~~~~~~~~~~~~~~~~~~~
> 236 | Assertion about to fail! logPP= %d\n", logPP);
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~
> | |
> | double
> hmmMiscFunctions.c: In function ‘UpdateGamma’:
> hmmMiscFunctions.c:274:27: warning: implicit declaration of function
> ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
> 274 | double *shape= (double*)Calloc(1, double);
> | ^~~~~~
> | calloc
> hmmMiscFunctions.c:274:37: error: expected expression before ‘double’
> 274 | double *shape= (double*)Calloc(1, double);
> | ^~~~~~
> hmmMiscFunctions.c:275:37: error: expected expression before ‘double’
> 275 | double *scale= (double*)Calloc(1, double);
> | ^~~~~~
> hmmMiscFunctions.c:287:3: warning: implicit declaration of function
> ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration]
> 287 | Free(shape);
> | ^~~~
> | free
> hmmMiscFunctions.c: In function ‘SStatsNormExp’:
> hmmMiscFunctions.c:384:10: warning: unused variable ‘wi’
> [-Wunused-variable]
> 384 | double wi, *newEx;
> | ^~
> hmmMiscFunctions.c: In function ‘UpdateNormExp’:
> hmmMiscFunctions.c:417:10: warning: unused variable ‘epsilon’
> [-Wunused-variable]
> 417 | double epsilon=0.00001;
> | ^~~~~~~
> In file included from hmmHeader.h:36,
> from hmmMiscFunctions.c:43:
> UsefulValues.h: At top level:
> UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not
> used [-Wunused-variable]
> 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
> | ^~~~~~~~~~~~~~~~~~~~~~~
> make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195:
> hmmMiscFunctions.o] Error 1
> ERROR: compilation failed for package ‘groHMM’
> * removing ‘/tmp/RtmpELy2EB/Rinst1165062fc12e4/groHMM’
> -----------------------------------
> ERROR: package installation failed
>
>
> I haven't changed anything in the package.
>
> Regards,
> Tulip.
>
>
> ________________________________
> From: James W. MacDonald <jmac...@uw.edu>
> Sent: Tuesday, December 3, 2024 2:31 PM
> To: Tulip Nandu <tulip.na...@utsouthwestern.edu>; Mike Smith <
> grimbo...@gmail.com>
> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
> Subject: RE: [Bioc-devel] groHMM package error
>
> You need to commit your changes to g...@git.bioconductor.org, which you
> apparently have not done as yet (you should have g...@git.bioconductor.org
> set up as a remote which you can see by doing git remote -v). The last
> commit is Jennifer Wokaty bumping the version for the last release:
>
> /groHMM$ git log
> commit a68457648cdef96ae2a8f40c484496e935d0fcb3 (HEAD -> devel,
> origin/master, origin/devel, origin/HEAD)
> Author: J Wokaty <jennifer.wok...@sph.cuny.edu>
> Date: Tue Oct 29 09:56:11 2024 -0400
>
> bump x.y.z version to odd y following creation of RELEASE_3_20 branch
>
> You also need to bump the version number in order to get the new version
> to build. You also need to make changes to the RELEASE_3_20 branch if you
> want the fix to propagate to the release version of your package. Please
> see the git version control section of the development pages
> https://urldefense.com/v3/__https://contributions.bioconductor.org/git-version-control.html__;!!MznTZTSvDXGV0Co!D1Ec1At0koOWiqp-WDw8kmv5F2XS6u9FgDh9_6bOg6sahspYVpDQH4VMAWnhLzWraEuUptCNTFhuhD3a6ZVoPFJgJ1w$
>
>
> -----Original Message-----
> From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of Tulip
> Nandu
> Sent: Tuesday, December 3, 2024 3:14 PM
> To: Mike Smith <grimbo...@gmail.com>
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] groHMM package error
>
> Hi,
>
> I edited the file based on Mike' s suggestion on the git page (image1) but
> doesn't seem to reflect when I clone the file using the git clone
> bioconductor package yet. Can someone confirm it will be done and nothing
> else I have to do from my end.
>
> Let me know.
>
> Regards,
> Tulip.
>
>
>
> ________________________________
> From: Mike Smith <grimbo...@gmail.com>
> Sent: Tuesday, November 26, 2024 2:50 AM
> To: Tulip Nandu <tulip.na...@utsouthwestern.edu>
> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] groHMM package error
>
>
> EXTERNAL MAIL
>
> Dear Tulip,
>
> The decideTestsDGE() function was deprecated in edgeR 4.2 and removed in
> the new 4.4 release. You can find some notes ion this n the NEWS at
> https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!K-Hz7m0Vt54!ml36G27n5i71mmZqYh9kGx64fb8MnMWqcgTRb-IOUtzTvcuIr8z00917gwIae3eKB558z662Sqs-Iu35-pnRAO0wmBtwCQ$
> <
> https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEQx-jd1t$
> >
>
> It looks to me like you should be able to use decideTests() as a drop in
> replacement in your package.
>
> Best,
> Mike
>
> On Mon, 25 Nov 2024 at 23:23, Tulip Nandu <tulip.na...@utsouthwestern.edu
> <mailto:tulip.na...@utsouthwestern.edu>> wrote:
> Hi,
>
> I keep getting this message from Bioconductor for groHMM package and don't
> know what the error is since I haven't changed anything in the package. Can
> someone please help?
>
> Regards,
> Tulip.
>
>
>
>
> "Warning in makeConsensusAnnotations(kgChr7, keytype = "gene_id", mc.cores
> = getOption("mc.cores")) :
> 562 ranges do not have gene_id and they are
> dropped
> Reduce isoforms(701) ... OK
> Truncate overlapped ranges ... OK
>
> 'select()' returned 1:1 mapping between keys and columns Calculate
> overlapping ... OK Scale overlapping ... OK
> Warning: file stem
> ‘/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpkfITSx/Rbuild130dca6dd2fd85/groHMM/vignettes/groHMM-fig2’
> is not portable Calculate overlapping ... OK Scale overlapping ... OK
> Loading required package: limma
>
> Attaching package: ‘limma’
>
> The following object is masked from ‘package:BiocGenerics’:
>
> plotMA
>
>
> Error: processing vignette 'groHMM.Rnw' failed with diagnostics:
> chunk 21 (label = DE for trascripts)
> Error in decideTestsDGE(et, p = 0.001, adjust = "fdr") :
> could not find function "decideTestsDGE"
>
> --- failed re-building ‘groHMM.Rnw’
>
> SUMMARY: processing the following file failed:
> ‘groHMM.Rnw’
>
> Error: Vignette re-building failed.
> Execution halted"
>
>
>
>
> ________________________________
>
> UT Southwestern
>
> Medical Center
>
> The future of medicine, today.
>
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> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEdQf2Ngg$
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