Jiefei Wang
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/gpuMagic |
| git_branch: devel |
| git_last_commit: 06a3340 |
| git_last_commit_date: 2024-10-29 10:37:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 889/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gpuMagic 1.23.0 (landing page) Jiefei Wang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the gpuMagic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gpuMagic.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: gpuMagic |
| Version: 1.23.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL gpuMagic |
| StartedAt: 2024-12-23 19:56:55 -0000 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 19:56:59 -0000 (Mon, 23 Dec 2024) |
| EllapsedTime: 4.2 seconds |
| RetCode: 1 |
| Status: ERROR |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL gpuMagic
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘gpuMagic’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/R/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c C_Interface.cpp -o C_Interface.o
C_Interface.cpp: In function ‘SEXPREC* getPlatformNum()’:
C_Interface.cpp:16:28: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
16 | SEXP platformNum = ScalarInteger(kernelManager::getPlatformNum());
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
C_Interface.cpp: In function ‘SEXPREC* getDeviceNum(SEXP)’:
C_Interface.cpp:22:68: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
22 | SEXP deviceNum = ScalarInteger(kernelManager::getDeviceNum(asInteger(platform)));
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:22:26: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
22 | SEXP deviceNum = ScalarInteger(kernelManager::getDeviceNum(asInteger(platform)));
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
C_Interface.cpp: In function ‘SEXPREC* getDeviceInfo(SEXP, SEXP)’:
C_Interface.cpp:28:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
28 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
In file included from C_Interface.h:4,
from C_Interface.cpp:10:
C_Interface.cpp:30:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
30 | SEXP info_R = PROTECT(allocVector(VECSXP, 8));
| ^~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
C_Interface.cpp:32:43: error: ‘mkString’ was not declared in this scope; did you mean ‘asString’?
32 | SET_VECTOR_ELT(info_R, 0, PROTECT(mkString(info.device_name.c_str())));
| ^~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
C_Interface.cpp:33:43: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
33 | SET_VECTOR_ELT(info_R, 1, PROTECT(ScalarInteger(info.device_type)));
| ^~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
C_Interface.cpp:34:43: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’?
34 | SET_VECTOR_ELT(info_R, 2, PROTECT(ScalarReal(info.global_memory)));
| ^~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
C_Interface.cpp:36:43: error: ‘ScalarLogical’ was not declared in this scope; did you mean ‘Rf_ScalarLogical’?
36 | SET_VECTOR_ELT(info_R, 4, PROTECT(ScalarLogical(info.has_local_memory)));
| ^~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
C_Interface.cpp:41:9: error: ‘unprotect’ was not declared in this scope; did you mean ‘Rf_unprotect’?
41 | unprotect(9);
| ^~~~~~~~~
| Rf_unprotect
C_Interface.cpp: In function ‘SEXPREC* upload(SEXP, SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:48:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
48 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:50:29: error: ‘asReal’ was not declared in this scope
50 | size_t dataLength = asReal(length);
| ^~~~~~
C_Interface.cpp:84:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
84 | error("Unsupported data structure!");
| ^~~~~
| perror
C_Interface.cpp: In function ‘SEXPREC* gpuMalloc(SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:96:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
96 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:97:47: error: ‘asReal’ was not declared in this scope
97 | openArray* matrix = new openArray(id, asReal(length), (dtype)asInteger(type));
| ^~~~~~
C_Interface.cpp: In function ‘SEXPREC* download(SEXP)’:
C_Interface.cpp:121:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
121 | res = PROTECT(allocVector(REALSXP, length));
| ^~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
C_Interface.cpp: In function ‘SEXPREC* hasKernel(SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:156:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
156 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope
12 | #define asString(x) string(CHAR(asChar(x)))
| ^~~~~~
/home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’
203 | #define CHAR(x) R_CHAR(x)
| ^
C_Interface.cpp:157:34: note: in expansion of macro ‘asString’
157 | programSignature sig = { asString(signature) ,string(),string(),asString(kernel) };
| ^~~~~~~~
C_Interface.cpp:158:20: error: ‘ScalarLogical’ was not declared in this scope; did you mean ‘Rf_ScalarLogical’?
158 | SEXP res = ScalarLogical(kernelManager::hasKernel(id, sig));
| ^~~~~~~~~~~~~
| Rf_ScalarLogical
C_Interface.cpp: In function ‘SEXPREC* createKernel(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:166:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
166 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope
12 | #define asString(x) string(CHAR(asChar(x)))
| ^~~~~~
/home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’
203 | #define CHAR(x) R_CHAR(x)
| ^
C_Interface.cpp:167:34: note: in expansion of macro ‘asString’
167 | programSignature sig = { asString(signature) ,asString(flag),asString(code),asString(kernel) };
| ^~~~~~~~
C_Interface.cpp: In function ‘SEXPREC* setParameter(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:178:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
178 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope
12 | #define asString(x) string(CHAR(asChar(x)))
| ^~~~~~
/home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’
203 | #define CHAR(x) R_CHAR(x)
| ^
C_Interface.cpp:179:34: note: in expansion of macro ‘asString’
179 | programSignature sig = { asString(signature),string(),string(),asString(kernel) };
| ^~~~~~~~
C_Interface.cpp: In function ‘SEXPREC* setSharedParameter(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:190:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
190 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope
12 | #define asString(x) string(CHAR(asChar(x)))
| ^~~~~~
/home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’
203 | #define CHAR(x) R_CHAR(x)
| ^
C_Interface.cpp:191:34: note: in expansion of macro ‘asString’
191 | programSignature sig = { asString(signature),string(),string(),asString(kernel) };
| ^~~~~~~~
C_Interface.cpp: In function ‘SEXPREC* launchKernel(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:203:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
203 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope
12 | #define asString(x) string(CHAR(asChar(x)))
| ^~~~~~
/home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’
203 | #define CHAR(x) R_CHAR(x)
| ^
C_Interface.cpp:205:34: note: in expansion of macro ‘asString’
205 | programSignature sig = { asString(signature),string(),string(),asString(kernel) };
| ^~~~~~~~
C_Interface.cpp: In function ‘SEXPREC* getPreferredGroupSize(SEXP, SEXP, SEXP, SEXP)’:
C_Interface.cpp:230:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
230 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:12:33: error: ‘asChar’ was not declared in this scope
12 | #define asString(x) string(CHAR(asChar(x)))
| ^~~~~~
/home/biocbuild/R/R/include/Rinternals.h:203:24: note: in definition of macro ‘CHAR’
203 | #define CHAR(x) R_CHAR(x)
| ^
C_Interface.cpp:231:34: note: in expansion of macro ‘asString’
231 | programSignature sig = { asString(signature),string(),string(),asString(kernel) };
| ^~~~~~~~
C_Interface.cpp:239:20: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
239 | SEXP res = ScalarInteger(prefferedSize);
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
C_Interface.cpp: In function ‘SEXPREC* getDeviceStatus(SEXP, SEXP)’:
C_Interface.cpp:246:33: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
246 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
C_Interface.cpp:252:24: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
252 | return(ScalarInteger(status));
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
C_Interface.cpp:272:16: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
272 | return(ScalarInteger(status));
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
C_Interface.cpp: In function ‘SEXPREC* getTrueAd(SEXP)’:
C_Interface.cpp:281:16: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’?
281 | return(ScalarReal(ad_double));
| ^~~~~~~~~~
| Rf_ScalarReal
C_Interface.cpp: In function ‘SEXPREC* asMatrix(SEXP, SEXP)’:
C_Interface.cpp:286:9: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’?
286 | setAttrib(data, R_DimSymbol, dim);
| ^~~~~~~~~
| Rf_setAttrib
C_Interface.cpp: In function ‘SEXPREC* getDeviceFullInfo(SEXP, SEXP)’:
C_Interface.cpp:292:27: error: ‘asInteger’ was not declared in this scope; did you mean ‘Rf_asInteger’?
292 | deviceIdentifier id = { asInteger(platform) ,asInteger(device) };
| ^~~~~~~~~
| Rf_asInteger
make: *** [/home/biocbuild/R/R/etc/Makeconf:204: C_Interface.o] Error 1
ERROR: compilation failed for package ‘gpuMagic’
* removing ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/gpuMagic’