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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).

CHECK results for CNEr on machv2

To the developers/maintainers of the CNEr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNEr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 342/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.28.0  (landing page)
Ge Tan
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: RELEASE_3_13
git_last_commit: fdeac98
git_last_commit_date: 2021-05-19 12:02:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CNEr
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNEr_1.28.0.tar.gz
StartedAt: 2021-10-14 17:34:33 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 17:47:47 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 794.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CNEr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNEr_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CNEr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.28.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNEr’ can be installed ... WARNING
Found the following significant warnings:
  ucsc/common.c:2842:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2843:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2844:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2845:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2846:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2847:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2848:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2849:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2976:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2977:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2978:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2979:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2980:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2981:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2982:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
  ucsc/common.c:2983:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CNEr.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 17.6Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
* 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 R 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/CNEr/libs/CNEr.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
makeGRBs     386.000  3.470 389.778
plotCNEWidth  10.412  0.396  10.815
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/CNEr.Rcheck/00check.log’
for details.



Installation output

CNEr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNEr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CNEr’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c R_init_CNEr.c -o R_init_CNEr.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c utils.c -o utils.o
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
  int _binFirstShift = binFirstShift();
      ^
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
  int _binNextShift = binNextShift();
      ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c io.c -o io.o
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
  struct axt *axt=NULL, *curAxt;
                         ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ceScan.c -o ceScan.o
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
  int i, n;
         ^
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
  char rest, path[PATH_LEN];
       ^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
  struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                      ^
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
  struct slCNE *CNE, *nextCNE, *el_CNE;
                ^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
  struct slCNE *CNE;
                ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
  int nrCNE[nrThresholds], i;
      ^
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
  int nrCNE[nrThresholds], i;
                           ^
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
  int nrThresholds = GET_LENGTH(winSize);
      ^
8 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/axt.c -o ucsc/axt.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/base64.c -o ucsc/base64.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/binRange.c -o ucsc/binRange.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/bits.c -o ucsc/bits.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/chain.c -o ucsc/chain.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:472:16: warning: unused function 'cirTreeOverlaps' [-Wunused-function]
INLINE boolean cirTreeOverlaps(int qChrom, int qStart, int qEnd, 
               ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1982:18: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if ((*in == '"'))
             ~~~~^~~~~~
ucsc/common.c:1982:18: note: remove extraneous parentheses around the comparison to silence this warning
        if ((*in == '"'))
            ~    ^     ~
ucsc/common.c:1982:18: note: use '=' to turn this equality comparison into an assignment
        if ((*in == '"'))
                 ^~
                 =
ucsc/common.c:2842:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
             ^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2843:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
             ^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2844:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
             ^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2845:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
             ^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2846:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2847:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2848:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2849:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^       ~
ucsc/common.c:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2976:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
             ^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2977:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
             ^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2978:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
             ^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2979:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
             ^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2980:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2981:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2982:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
ucsc/common.c:2983:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^       ~
ucsc/common.c:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
                     ^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char   /* Wants to be unsigned 8 bits. */
              ^
17 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
                  ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/hash.c -o ucsc/hash.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/https.c -o ucsc/https.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/intExp.c -o ucsc/intExp.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/kxTok.c -o ucsc/kxTok.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/options.c -o ucsc/options.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/os.c -o ucsc/os.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include  -g -fPIC  -Wall -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CNEr.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-CNEr/00new/CNEr/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 (CNEr)

Tests output

CNEr.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CNEr)

> 
> test_check("CNEr")
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
 33.602   1.188  34.805 

Example timings

CNEr.Rcheck/CNEr-Ex.timings

nameusersystemelapsed
AssemblyStats0.0200.0320.078
Axt-class1.2290.0931.324
Axt-util0.1600.0020.163
CNE-class0.3330.0100.343
CNEDanRer10Hg380.0120.0020.013
CNEDensity1.1470.0231.172
GRangePairs-class1.3170.0261.345
addAncestorGO000
axisTrack0.0030.0030.005
axtChain0.0000.0000.001
axtInfo0.0010.0010.002
binner0.0040.0010.005
blatCNE000
ceScan-methods3.0810.1123.187
chainMergeSort0.0000.0000.001
chainNetSyntenic0.0000.0000.001
chainPreNet000
cneFinalListDanRer10Hg380.0500.0020.053
cneMerge1.5720.0171.589
fetchChromSizes0.0000.0010.001
fixCoordinates1.0630.0501.113
grangesPairsForDotplot0.0020.0010.003
last000
lastz0.0000.0010.000
lavToPsl000
makeAncoraFiles0.0410.0030.044
makeAxtTracks0.6010.0590.661
makeCNEDensity000
makeGRBs386.000 3.470389.778
matchDistribution0.4450.0050.450
netToAxt0.0000.0010.001
orgKEGGIds2EntrezIDs000
plotCNEDistribution0.6840.0100.694
plotCNEWidth10.412 0.39610.815
psubAxt0.7960.0270.822
read.rmMask.GRanges0.0550.0020.059
read.rmskFasta0.0590.0020.061
readAncora0.1870.0010.188
readAncoraIntoSQLite1.3580.0241.384
readAxt0.1790.0050.185
readBed0.1310.0080.137
readCNERangesFromSQLite0.1340.0050.139
reverseCigar0.0010.0010.001
saveCNEToSQLite0.1290.0050.135
scoringMatrix0.0010.0010.002
subAxt-methods1.7170.0291.747
syntenicDotplot2.1830.2522.330
writeAxt0.1890.0150.205