Nicholas Cooley
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: 88b8d0f |
| git_last_commit_date: 2024-10-29 10:46:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:40 -0500 (Mon, 25 Nov 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 2088/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.19.0 (landing page) Nicholas Cooley
| 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 | |||||||||
|
To the developers/maintainers of the SynExtend package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SynExtend |
| Version: 1.19.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SynExtend |
| StartedAt: 2024-11-24 18:55:02 -0500 (Sun, 24 Nov 2024) |
| EndedAt: 2024-11-24 18:55:05 -0500 (Sun, 24 Nov 2024) |
| EllapsedTime: 2.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SynExtend
###
##############################################################################
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* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* preparing ‘SynExtend’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDend.c -o CDend.o
CDend.c:265:29: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
unsigned int *allHashed = Calloc(numLabels, unsigned int);
^
CDend.c:265:47: error: expected expression
unsigned int *allHashed = Calloc(numLabels, unsigned int);
^
CDend.c:273:38: error: unexpected type name 'ulong': expected expression
ulong *keyvals = Calloc(numLabels, ulong);
^
CDend.c:274:29: error: unexpected type name 'ulong': expected expression
ulong *ht1 = Calloc(t1pl, ulong);
^
CDend.c:275:29: error: unexpected type name 'ulong': expected expression
ulong *ht2 = Calloc(t2pl, ulong);
^
CDend.c:290:3: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
Free(allHashed);
^
CDend.c:290:3: note: did you mean 'free'?
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/malloc/_malloc.h:42:7: note: 'free' declared here
void free(void *);
^
CDend.c:294:34: error: expected expression
int *idxToKeep1 = Calloc(t1pl, int);
^
CDend.c:295:34: error: expected expression
int *idxToKeep2 = Calloc(t2pl, int);
^
CDend.c:374:29: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
unsigned int *allHashed = Calloc(numLabels, unsigned int);
^
CDend.c:374:47: error: expected expression
unsigned int *allHashed = Calloc(numLabels, unsigned int);
^
CDend.c:382:38: error: unexpected type name 'ulong': expected expression
ulong *keyvals = Calloc(numLabels, ulong);
^
CDend.c:383:29: error: unexpected type name 'ulong': expected expression
ulong *ht1 = Calloc(t1pl, ulong);
^
CDend.c:384:29: error: unexpected type name 'ulong': expected expression
ulong *ht2 = Calloc(t2pl, ulong);
^
CDend.c:385:35: error: expected expression
double *dists1 = Calloc(t1pl+2, double);
^
CDend.c:386:35: error: expected expression
double *dists2 = Calloc(t2pl+2, double);
^
CDend.c:401:3: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
Free(allHashed);
^
CDend.c:412:34: error: expected expression
int *idxToKeep1 = Calloc(t1pl, int);
^
CDend.c:413:34: error: expected expression
int *idxToKeep2 = Calloc(t2pl, int);
^
CDend.c:496:20: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
double *scores = Calloc(head->value+1, double);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [CDend.o] Error 1
ERROR: compilation failed for package ‘SynExtend’
* removing ‘/private/tmp/RtmpaP2Cis/Rinstf417120b0fa0/SynExtend’
-----------------------------------
ERROR: package installation failed