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humlab-speech / visible-speech-deployment

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Kan inte kompilera superassp #201

Closed johanvonboer closed 4 months ago

johanvonboer commented 6 months ago

image

image

Felet uppstår när jag försöker bygga: https://github.com/humlab-speech/visible-speech-deployment/blob/master/docker/session-manager/operations-session/Dockerfile

FredrikKarlssonSpeech commented 6 months ago

Knepigt. Bygger finfint på min dator, och byggfelet är ju C-koden som jag inte rört.

Har just pushat till "master". Kan du bygga?

On Thu, May 2, 2024 at 4:32 PM Johan von Boer @.***> wrote:

image.png (view on web) https://github.com/humlab-speech/visible-speech-deployment/assets/34707290/1259f5f0-e451-4eeb-93d6-623e90fcc133

image.png (view on web) https://github.com/humlab-speech/visible-speech-deployment/assets/34707290/5f62243c-9aef-41a7-9055-9e7cadba6a6e

Felet uppstår när jag försöker bygga:

https://github.com/humlab-speech/visible-speech-deployment/blob/master/docker/session-manager/operations-session/Dockerfile

— Reply to this email directly, view it on GitHub https://github.com/humlab-speech/visible-speech-deployment/issues/201, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABQ4NXCC2K5YMAWO3H5S63ZAJE6HAVCNFSM6AAAAABHD3AJFWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3TKNRZGU2DENY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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johanvonboer commented 6 months ago

Funkar fortfarande inte att bygga för mig, testa gärna att klona ner repot och bygga på exakt samma sätt som mig, förutsatt att du har docker installerat så är det bara:

git clone https://github.com/humlab-speech/visible-speech-deployment
cd visible-speech-deployment/docker/session-manager
docker build -t visp-operations-session --no-cache -f operations-session/Dockerfile .
FredrikKarlssonSpeech commented 6 months ago

Jag kör fast ett fel innan detta, som har med rosetta att göra tror jag:

% docker build -t visp-operations-session --no-cache -f operations-session/Dockerfile .
[+] Building 28.2s (15/33)                                                                                                                                        docker:desktop-linux
 => [internal] load build definition from Dockerfile                                                                                                                              0.0s
 => => transferring dockerfile: 4.13kB                                                                                                                                            0.0s
 => [internal] load metadata for docker.io/rocker/rstudio:4                                                                                                                       1.2s
 => [internal] load .dockerignore                                                                                                                                                 0.0s
 => => transferring context: 2B                                                                                                                                                   0.0s
 => CACHED [base  1/15] FROM docker.io/rocker/rstudio:4@sha256:c0707bd7a9a28db2eca72e24c334d71a16898ad1e155cc2b5f5db89f70234570                                                   0.0s
 => [internal] load build context                                                                                                                                                 0.0s
 => => transferring context: 229B                                                                                                                                                 0.0s
 => [final  5/11] ADD https://www.random.org/cgi-bin/randbyte?nbytes=10&format=h skipcache                                                                                        0.3s
 => [base  2/15] RUN sed -i 's/archive.ubuntu.com/se.archive.ubuntu.com/g' /etc/apt/sources.list                                                                                  0.2s
 => [base  3/15] RUN apt-get update && apt-get install -y curl ca-certificates gnupg                                                                                              6.4s
 => [base  4/15] RUN mkdir -p /etc/apt/keyrings                                                                                                                                   0.1s 
 => [base  5/15] RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg                                     0.3s 
 => [base  6/15] RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_20.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list     0.1s 
 => [base  7/15] RUN apt-get update                                                                                                                                               1.0s 
 => [base  8/15] RUN apt-get install nodejs -y                                                                                                                                    5.6s 
 => [base  9/15] RUN curl -o Miniconda3-latest-Linux-x86_64.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh                                             12.8s 
 => ERROR [base 10/15] RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b                                                                                                            0.5s 
------                                                                                                                                                                                 
 > [base 10/15] RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b:                                                                                                                       
0.124 PREFIX=/root/miniconda3                                                                                                                                                          
0.475 Unpacking payload ...                                                                                                                                                            
0.477 rosetta error: failed to open elf at /lib64/ld-linux-x86-64.so.2
0.477  ./Miniconda3-latest-Linux-x86_64.sh: line 1140:    42 Exit 141                extract_range $boundary1 $boundary2
0.477         43 Trace/breakpoint trap   | CONDA_QUIET="$BATCH" "$CONDA_EXEC" constructor --extract-tarball --prefix "$PREFIX"
------
Dockerfile:22
--------------------
  20 |     
  21 |     RUN curl -o Miniconda3-latest-Linux-x86_64.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  22 | >>> RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b
  23 |     RUN /root/miniconda3/bin/conda install mamba -n base -c conda-forge
  24 |     
--------------------
ERROR: failed to solve: process "/bin/sh -c bash ./Miniconda3-latest-Linux-x86_64.sh -b" did not complete successfully: exit code: 133
FredrikKarlssonSpeech commented 5 months ago

Bara för att återföra mina fynd under dagarna i veckan. Jag kan inte återskapa problemet utanför docker. Paketet bygger finfint.

> devtools::install_github("humlab-speech/superassp")
Downloading GitHub repo humlab-speech/superassp@HEAD
'/usr/bin/git' clone --depth 1 --no-hardlinks --recurse-submodules https://github.com/sp-nitech/SPTK.git /var/folders/lr/h3mlkmq540d6xjrh3bpdms600000gn/T//Rtmpy4Zt1y/remotes14501376f90bb/humlab-speech-superassp-7a29c98/src/SPTK
Cloning into '/var/folders/lr/h3mlkmq540d6xjrh3bpdms600000gn/T//Rtmpy4Zt1y/remotes14501376f90bb/humlab-speech-superassp-7a29c98/src/SPTK'...
remote: Enumerating objects: 889, done.
remote: Counting objects: 100% (889/889), done.
remote: Compressing objects: 100% (709/709), done.
remote: Total 889 (delta 490), reused 350 (delta 152), pack-reused 0
Receiving objects: 100% (889/889), 1.08 MiB | 5.16 MiB/s, done.
Resolving deltas: 100% (490/490), done.
'/usr/bin/git' clone --depth 1 --no-hardlinks --recurse-submodules https://github.com/festvox/speech_tools /var/folders/lr/h3mlkmq540d6xjrh3bpdms600000gn/T//Rtmpy4Zt1y/remotes14501376f90bb/humlab-speech-superassp-7a29c98/src/ESTK
Cloning into '/var/folders/lr/h3mlkmq540d6xjrh3bpdms600000gn/T//Rtmpy4Zt1y/remotes14501376f90bb/humlab-speech-superassp-7a29c98/src/ESTK'...
remote: Enumerating objects: 1023, done.
remote: Counting objects: 100% (1023/1023), done.
remote: Compressing objects: 100% (773/773), done.
remote: Total 1023 (delta 490), reused 514 (delta 241), pack-reused 0
Receiving objects: 100% (1023/1023), 1.64 MiB | 5.97 MiB/s, done.
Resolving deltas: 100% (490/490), done.
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                 
 2: CRAN packages only                  
 3: None                                
 4: rlang      (1.1.1  -> 1.1.3 ) [CRAN]
 5: lifecycle  (1.0.3  -> 1.0.4 ) [CRAN]
 6: glue       (1.6.2  -> 1.7.0 ) [CRAN]
 7: cli        (3.6.1  -> 3.6.2 ) [CRAN]
 8: R.oo       (1.25.0 -> 1.26.0) [CRAN]
 9: rprojroot  (2.0.3  -> 2.0.4 ) [CRAN]
10: Rcpp       (1.0.11 -> 1.0.12) [CRAN]
11: fansi      (1.0.5  -> 1.0.6 ) [CRAN]
12: progress   (1.2.2  -> 1.2.3 ) [CRAN]
13: withr      (2.5.1  -> 3.0.0 ) [CRAN]
14: vctrs      (0.6.4  -> 0.6.5 ) [CRAN]
15: tidyselect (1.2.0  -> 1.2.1 ) [CRAN]
16: stringi    (1.7.12 -> 1.8.4 ) [CRAN]
17: R.utils    (2.12.2 -> 2.12.3) [CRAN]
18: jsonlite   (1.8.7  -> 1.8.8 ) [CRAN]
19: vroom      (1.6.4  -> 1.6.5 ) [CRAN]
20: stringr    (1.5.0  -> 1.5.1 ) [CRAN]
21: dplyr      (1.1.3  -> 1.1.4 ) [CRAN]
22: av         (0.8.6  -> 0.9.0 ) [CRAN]
23: uuid       (1.1-1  -> 1.2-0 ) [CRAN]
24: logger     (0.2.2  -> 0.3.0 ) [CRAN]
25: digest     (0.6.33 -> 0.6.35) [CRAN]
26: reticulate (1.34.0 -> 1.36.1) [CRAN]
27: Rdpack     (2.5    -> 2.6   ) [CRAN]
28: readr      (2.1.4  -> 2.1.5 ) [CRAN]
29: tidyr      (1.3.0  -> 1.3.1 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
rlang      (1.1.1  -> 1.1.3 ) [CRAN]
lifecycle  (1.0.3  -> 1.0.4 ) [CRAN]
glue       (1.6.2  -> 1.7.0 ) [CRAN]
cli        (3.6.1  -> 3.6.2 ) [CRAN]
R.oo       (1.25.0 -> 1.26.0) [CRAN]
rprojroot  (2.0.3  -> 2.0.4 ) [CRAN]
Rcpp       (1.0.11 -> 1.0.12) [CRAN]
fansi      (1.0.5  -> 1.0.6 ) [CRAN]
progress   (1.2.2  -> 1.2.3 ) [CRAN]
withr      (2.5.1  -> 3.0.0 ) [CRAN]
vctrs      (0.6.4  -> 0.6.5 ) [CRAN]
tidyselect (1.2.0  -> 1.2.1 ) [CRAN]
stringi    (1.7.12 -> 1.8.4 ) [CRAN]
R.utils    (2.12.2 -> 2.12.3) [CRAN]
jsonlite   (1.8.7  -> 1.8.8 ) [CRAN]
vroom      (1.6.4  -> 1.6.5 ) [CRAN]
stringr    (1.5.0  -> 1.5.1 ) [CRAN]
dplyr      (1.1.3  -> 1.1.4 ) [CRAN]
av         (0.8.6  -> 0.9.0 ) [CRAN]
uuid       (1.1-1  -> 1.2-0 ) [CRAN]
logger     (0.2.2  -> 0.3.0 ) [CRAN]
digest     (0.6.33 -> 0.6.35) [CRAN]
reticulate (1.34.0 -> 1.36.1) [CRAN]
Rdpack     (2.5    -> 2.6   ) [CRAN]
readr      (2.1.4  -> 2.1.5 ) [CRAN]
tidyr      (1.3.0  -> 1.3.1 ) [CRAN]
Installing 26 packages: rlang, lifecycle, glue, cli, R.oo, rprojroot, Rcpp, fansi, progress, withr, vctrs, tidyselect, stringi, R.utils, jsonlite, vroom, stringr, dplyr, av, uuid, logger, digest, reticulate, Rdpack, readr, tidyr
trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/rlang_1.1.3.tgz'
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The downloaded binary packages are in
    /var/folders/lr/h3mlkmq540d6xjrh3bpdms600000gn/T//Rtmpy4Zt1y/downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
   checking for file ‘/private/var/folders/lr/h3mlkmq540d6xjrh3bpdms600000gn/T/R✔  checking for file ‘/private/var/folders/lr/h3mlkmq540d6xjrh3bpdms600000gn/T/Rtmpy4Zt1y/remotes14501376f90bb/humlab-speech-superassp-7a29c98/DESCRIPTION’
─  preparing ‘superassp’: (1.4s)
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to process help pages (341ms)
   Loading required namespace: superassp
─  saving partial Rd database (677ms)
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories (6s)
─  building ‘superassp_0.4.0.tar.gz’

* installing *source* package ‘superassp’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I assp -DWRASSP -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dataobj.c -o dataobj.o
dataobj.c:56:21: warning: variable 'i' set but not used
      [-Wunused-but-set-variable]
    int             i;
                    ^
dataobj.c:170:21: warning: unused variable 'genVar'
      [-Wunused-variable]
    TSSFF_Generic  *genVar = NULL;
                    ^
dataobj.c:397:21: warning: variable 'i' set but not used
      [-Wunused-but-set-variable]
    int             i,
                    ^
dataobj.c:405:21: warning: variable 'i8Ptr' set but not
      used [-Wunused-but-set-variable]
    int8_t         *i8Ptr;
                    ^
dataobj.c:602:21: warning: unused variable 'numFields'
      [-Wunused-variable]
    size_t          numFields = -1;
                    ^
dataobj.c:608:21: warning: unused variable 'varNames'
      [-Wunused-variable]
                    varNames;
                    ^
dataobj.c:886:21: warning: variable 'i' set but not used
      [-Wunused-but-set-variable]
    int             i,
                    ^
dataobj.c:894:21: warning: variable 'i8Ptr' set but not
      used [-Wunused-but-set-variable]
    int8_t         *i8Ptr;
                    ^
dataobj.c:142:1: warning: unused function 'DObjFinalizer'
      [-Wunused-function]
DObjFinalizer(SEXP dPtr)
^
9 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I assp -DWRASSP -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c performAssp.c -o performAssp.o
performAssp.c:552:12: warning: variable 'i' set but not
      used [-Wunused-but-set-variable]
  for (int i = 0; args != R_NilValue; i++, args = CDR(args)) {
           ^
performAssp.c:487:3: warning: variable 'pBar' set but not
      used [-Wunused-but-set-variable]
  pBar = R_NilValue,
  ^
performAssp.c:488:3: warning: unused variable
      'utilsPackage' [-Wunused-variable]
  utilsPackage,           /* to update the prograssbar */
  ^
performAssp.c:489:1: warning: unused variable 'newVal'
      [-Wunused-variable]
newVal,
^
performAssp.c:490:1: warning: unused variable 'R_fcall1'
      [-Wunused-variable]
R_fcall1, R_fcall2, R_fcall3; // for protected versions 
^
performAssp.c:490:11: warning: unused variable 'R_fcall2'
      [-Wunused-variable]
R_fcall1, R_fcall2, R_fcall3; // for protected versions 
          ^
performAssp.c:490:21: warning: unused variable 'R_fcall3'
      [-Wunused-variable]
R_fcall1, R_fcall2, R_fcall3; // for protected versions 
                    ^
performAssp.c:1207:21: warning: variable 'FILE_IN' set but
      not used [-Wunused-but-set-variable]
    int             FILE_IN,
                    ^
8 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I assp -DWRASSP -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c types.c -o types.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I assp -DWRASSP -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c superassp_init.c -o superassp_init.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o superassp.so assp/acf.o assp/dataobj.o assp/freqconv.o assp/mhs.o assp/smp2dur.o assp/asspana.o assp/diff.o assp/headers.o assp/miscstring.o assp/spectra.o assp/asspfio.o assp/dsputils.o assp/isgerman.o assp/myrand.o assp/statistics.o assp/asspmess.o assp/fft.o assp/ksv.o assp/myrint.o assp/trace.o assp/aucheck.o assp/fgetl.o assp/labelobj.o assp/numdecim.o assp/winfuncs.o assp/auconv.o assp/filter.o assp/lpc.o assp/parsepath.o assp/zcr.o assp/bitarray.o assp/filters.o assp/math.o assp/rfc.o assp/chain.o assp/fmt.o assp/memswab.o assp/rms.o dataobj.o performAssp.o types.o superassp_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -single_module is obsolete
ld: warning: -multiply_defined is obsolete
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-superassp/00new/superassp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (superassp)

Och tar jag bort superassp och reindeer ur Dockerfile så klagar den på att den inte kan installera "devtools"?? 

% ./build-operations-session.sh    
[+] Building 236.6s (19/27)                                                                                                                                       docker:desktop-linux
 => [internal] load build definition from Dockerfile                                                                                                                              0.0s
 => => transferring dockerfile: 3.60kB                                                                                                                                            0.0s
 => [internal] load metadata for docker.io/rocker/rstudio:4                                                                                                                       1.1s
 => [internal] load .dockerignore                                                                                                                                                 0.0s
 => => transferring context: 2B                                                                                                                                                   0.0s
 => [final  5/10] ADD https://www.random.org/cgi-bin/randbyte?nbytes=10&format=h skipcache                                                                                        0.4s
 => [base  1/10] FROM docker.io/rocker/rstudio:4@sha256:d556954973f5cfb87abfe0708be606d9812f3c2769ae884a6969cc75abfd50d4                                                          0.0s
 => [internal] load build context                                                                                                                                                 0.0s
 => => transferring context: 229B                                                                                                                                                 0.0s
 => CACHED [base  2/10] RUN sed -i 's/archive.ubuntu.com/se.archive.ubuntu.com/g' /etc/apt/sources.list                                                                           0.0s
 => CACHED [base  3/10] RUN apt-get update && apt-get install -y curl ca-certificates gnupg                                                                                       0.0s
 => CACHED [base  4/10] RUN mkdir -p /etc/apt/keyrings                                                                                                                            0.0s
 => CACHED [base  5/10] RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg                              0.0s
 => CACHED [base  6/10] RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_20.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.  0.0s
 => CACHED [base  7/10] RUN apt-get update                                                                                                                                        0.0s
 => CACHED [base  8/10] RUN apt-get install nodejs -y                                                                                                                             0.0s
 => CACHED [base  9/10] RUN rm /etc/localtime &&     ln -s /usr/share/zoneinfo/Europe/Stockholm /etc/localtime &&     apt-get update &&     apt-get install -y zlib1g-dev nano c  0.0s
 => CACHED [base 10/10] WORKDIR /home/rstudio                                                                                                                                     0.0s
 => [r_packages 1/1] RUN echo 'chooseCRANmirror(graphics=FALSE, ind=62);install.packages(c("git2r", "openxlsx", "ggpubr", "gt", "tidyverse", "tidymodels", "devtools","emuR","r  52.8s
 => [python_packages 1/1] RUN pip install --upgrade pip &&     pip install --prefer-binary numpy &&     pip install --prefer-binary torch torchvision torchaudio --extra-index  182.4s
 => [matlab 1/1] WORKDIR /home/rstudio                                                                                                                                            0.0s 
 => ERROR [final  1/10] RUN echo 'devtools::install_github("humlab-speech/reindeer", dependencies = TRUE)' | R --save                                                             0.2s 
------                                                                                                                                                                                 
 > [final  1/10] RUN echo 'devtools::install_github("humlab-speech/reindeer", dependencies = TRUE)' | R --save:                                                                        
0.162                                                                                                                                                                                  
0.162 R version 4.4.0 (2024-04-24) -- "Puppy Cup"                                                                                                                                      
0.162 Copyright (C) 2024 The R Foundation for Statistical Computing                                                                                                                    
0.162 Platform: aarch64-unknown-linux-gnu                                                                                                                                              
0.162 
0.162 R is free software and comes with ABSOLUTELY NO WARRANTY.
0.162 You are welcome to redistribute it under certain conditions.
0.162 Type 'license()' or 'licence()' for distribution details.
0.162 
0.162   Natural language support but running in an English locale
0.162 
0.162 R is a collaborative project with many contributors.
0.162 Type 'contributors()' for more information and
0.162 'citation()' on how to cite R or R packages in publications.
0.162 
0.162 Type 'demo()' for some demos, 'help()' for on-line help, or
0.162 'help.start()' for an HTML browser interface to help.
0.162 Type 'q()' to quit R.
0.162 
0.220 > devtools::install_github("humlab-speech/reindeer", dependencies = TRUE)
0.221 Error in loadNamespace(x) : there is no package called ‘devtools’
0.221 Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
0.221 Execution halted

Hur ser det ut för er då?

FredrikKarlssonSpeech commented 5 months ago

Ett del-problem, även om det inte rör devtools-saken, är att kompilatorn inte längre verkar acceptera C-koden i superassp:

820.2 dataobj.c: In function ‘getDObj’:
820.2 dataobj.c:27:9: error: format not a string literal and no format arguments [-Werror=format-security]
820.2    27 |         error(getAsspMsg(asspMsgNum));
820.2       |         ^~~~~
820.2 dataobj.c:34:9: error: format not a string literal and no format arguments [-Werror=format-security]
820.2    34 |         error(getAsspMsg(asspMsgNum));
820.2       |         ^~~~~
820.2 dataobj.c: In function ‘getDObj2’:
820.2 dataobj.c:126:9: error: format not a string literal and no format arguments [-Werror=format-security]
820.2   126 |         error(getAsspMsg(asspMsgNum));
820.2       |         ^~~~~
820.2 dataobj.c: In function ‘dobj2AsspDataObj’:
820.2 dataobj.c:170:21: warning: unused variable ‘genVar’ [-Wunused-variable]
820.2   170 |     TSSFF_Generic  *genVar = NULL;
820.2       |                     ^~~~~~
820.2 dataobj.c: In function ‘getDObjTrackData’:
820.2 dataobj.c:405:21: warning: variable ‘i8Ptr’ set but not used [-Wunused-but-set-variable]
820.2   405 |     int8_t         *i8Ptr;
820.2       |                     ^~~~~
820.2 dataobj.c:397:21: warning: variable ‘i’ set but not used [-Wunused-but-set-variable]
820.2   397 |     int             i,
820.2       |                     ^
820.2 dataobj.c: In function ‘sexp2dobj’:
820.2 dataobj.c:633:9: error: format not a string literal and no format arguments [-Werror=format-security]
820.2   633 |         error(getAsspMsg(asspMsgNum));
820.2       |         ^~~~~
820.2 dataobj.c:768:17: error: format not a string literal and no format arguments [-Werror=format-security]
820.2   768 |                 error(getAsspMsg(asspMsgNum));
820.2       |                 ^~~~~
820.2 dataobj.c:772:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
820.2   772 |                 error("Dimensions of tracks do not match."
820.2       |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
820.2   773 |                       "(%d rows in first track, but %d rows in track %d).",
820.2   774 |                       dop->numRecords, INTEGER(attr)[0], i);
820.2       |                       ~~~~~~~~~~~~~~~
820.2       |                          |
820.2       |                          long int
820.2 dataobj.c:773:26: note: format string is defined here
820.2   773 |                       "(%d rows in first track, but %d rows in track %d).",
820.2       |                         ~^
820.2       |                          |
820.2       |                          int
820.2       |                         %ld
820.2 dataobj.c:842:9: error: format not a string literal and no format arguments [-Werror=format-security]
820.2   842 |         error(getAsspMsg(asspMsgNum));
820.2       |         ^~~~~
820.2 dataobj.c:608:21: warning: unused variable ‘varNames’ [-Wunused-variable]
820.2   608 |                     varNames;
820.2       |                     ^~~~~~~~
820.2 dataobj.c:602:21: warning: unused variable ‘numFields’ [-Wunused-variable]
820.2   602 |     size_t          numFields = -1;
820.2       |                     ^~~~~~~~~
820.2 dataobj.c: In function ‘writeDObj_’:
820.2 dataobj.c:868:9: error: format not a string literal and no format arguments [-Werror=format-security]
820.2   868 |         error(getAsspMsg(asspMsgNum));
820.2       |         ^~~~~
820.2 dataobj.c: In function ‘addTrackData’:
820.2 dataobj.c:894:21: warning: variable ‘i8Ptr’ set but not used [-Wunused-but-set-variable]
820.2   894 |     int8_t         *i8Ptr;
820.2       |                     ^~~~~
820.2 dataobj.c:886:21: warning: variable ‘i’ set but not used [-Wunused-but-set-variable]
820.2   886 |     int             i,
820.2       |                     ^
820.2 At top level:
820.2 dataobj.c:142:1: warning: ‘DObjFinalizer’ defined but not used [-Wunused-function]
820.2   142 | DObjFinalizer(SEXP dPtr)
820.2       | ^~~~~~~~~~~~~
820.2 dataobj.c: In function ‘getDObjTrackData’:
820.2 dataobj.c:404:21: warning: ‘u8Ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
820.2   404 |     uint8_t        *u8Ptr;
820.2       |                     ^~~~~
820.2 dataobj.c:414:21: warning: ‘Ians’ may be used uninitialized in this function [-Wmaybe-uninitialized]
820.2   414 |     int            *Ians;
820.2       |                     ^~~~
820.2 dataobj.c:413:21: warning: ‘Rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
820.2   413 |     double         *Rans;
820.2       |                     ^~~~
820.2 dataobj.c: In function ‘addTrackData’:
820.2 dataobj.c:933:30: warning: ‘u8Ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
820.2   933 |                     u8Ptr[n] = (int8_t) numPtr[m + n * dop->numRecords];
820.2       |                     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
820.2 cc1: some warnings being treated as errors
820.2 make: *** [/usr/local/lib/R/etc/Makeconf:195: dataobj.o] Error 1

även om processen inte verkar stanna upp just på grund av detta. Men man ser att "cc1" används, kan vi använda clang istället i denna kompilering möjligtvis @TomasSkotare ?

FredrikKarlssonSpeech commented 5 months ago

@TomasSkotare @johanvonboer

Den version jag just skickade in https://github.com/humlab-speech/visible-speech-deployment/commit/0c340e8299c98e816e15f9e12aa1efd7fd6bd2a8 löser inte problemet, men miljön bör kunna byggas (på era datorer, inte min) så att jag kan få en miljö att undersöka varför supeassp inte bygger i docker-miljön, men väl fungerar på min dator. Det har nog att göra med kompileringen av C-koden att göra, tror jag, men jag kan inte undersöka vidare utan att kunna få sitta i miljön.

FredrikKarlssonSpeech commented 4 months ago

Verkar vara löst till den nivån att den paketet bygger i användarens miljö i alla fall. Kan du testa om du kan lägga till superassp och reindeer i imagen igen @TomasSkotare ?

TomasSkotare commented 4 months ago

Detta är fixat och ska vara med i senaste imagen!