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This page was generated on 2025-10-24 12:06 -0400 (Fri, 24 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4898
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4688
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4634
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
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 1081/2359HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iscream 0.99.7  (landing page)
James Eapen
Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025)
git_url: https://git.bioconductor.org/packages/iscream
git_branch: devel
git_last_commit: bfe73bb
git_last_commit_date: 2025-10-21 11:10:12 -0400 (Tue, 21 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    NA    NA  

CHECK results for iscream on kjohnson3

To the developers/maintainers of the iscream package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iscream.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.

raw results


Summary

Package: iscream
Version: 0.99.7
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iscream.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iscream_0.99.7.tar.gz
StartedAt: 2025-10-23 20:27:02 -0400 (Thu, 23 Oct 2025)
EndedAt: 2025-10-23 20:27:35 -0400 (Thu, 23 Oct 2025)
EllapsedTime: 32.4 seconds
RetCode: 0
Status:   OK  
CheckDir: iscream.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iscream.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iscream_0.99.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/iscream.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iscream/DESCRIPTION’ ... OK
* this is package ‘iscream’ version ‘0.99.7’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘iscream’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... OK
* checking installed package size ... OK
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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 line endings in shell scripts ... 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/4.5-arm64/Resources/library/iscream/libs/iscream.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (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 nor [v]sprintf. 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/iscream.Rcheck/00check.log’
for details.

Installation output

iscream.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iscream
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘iscream’ ...
** this is package ‘iscream’ version ‘0.99.7’
** using staged installation
*** Configuring for package installation...
**** Trying pkg-config to use system htslib headers...
     Falling back to Rhtslib
     Using Rhtslib cflags and libs for htslib!
**** Using clang
     Apple clang version 15.0.0 (clang-1500.1.0.2.5)
     Target: arm64-apple-darwin22.6.0
     Thread model: posix
     InstalledDir: /Library/Developer/CommandLineTools/usr/bin
     WARNING: Could not find tabix to check for minimum htslib version - make sure its >= 1.17
**** Compilation flags
     Using PKG_CFLAGS=-D_FILE_OFFSET_BITS=64
     Using PKG_LIBS='/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a' -lcurl -lbz2 -llzma -lz
**** Checking if htslib was compiled with libdeflate
     NOTE: iscream queries may be slower with Rhtslib than with htslib compiled with libdeflate
     See <https://huishenlab.github.io/iscream/articles/htslib.html> for more information
**** Success!
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c decode_mat.cpp -o decode_mat.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c get_threads.cpp -o get_threads.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c log.cpp -o log.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c parsers.cpp -o parsers.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c query.cpp -o query.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c query_all.cpp -o query_all.o
In file included from query_all.cpp:1:
./query_all.hpp:56:1: warning: unused function 'khmap_destroy' [-Wunused-function]
KHASHL_MAP_INIT(static, khmap_t, khmap, CpG, int, kh_hash_cpg, kh_eq_cpg);
^
./../inst/include/khashl.h:350:13: note: expanded from macro 'KHASHL_MAP_INIT'
        SCOPE void prefix##_destroy(HType *h) { prefix##_m_destroy(h); } \
                   ^
<scratch space>:394:1: note: expanded from here
khmap_destroy
^
In file included from query_all.cpp:1:
./query_all.hpp:56:1: warning: unused function 'khmap_del' [-Wunused-function]
./../inst/include/khashl.h:352:12: note: expanded from macro 'KHASHL_MAP_INIT'
        SCOPE int prefix##_del(HType *h, khint_t k) { return prefix##_m_del(h, k); } \
                  ^
<scratch space>:399:1: note: expanded from here
khmap_del
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c summarize_regions.cpp -o summarize_regions.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o iscream.so RcppExports.o decode_mat.o get_threads.o log.o parsers.o query.o query_all.o summarize_regions.o /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-iscream/00new/iscream/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (iscream)

Tests output

iscream.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(iscream)
iscream using 1 thread by default but parallelly::availableCores() detects 2 possibly available threads. See `?set_threads` for information on multithreading before trying to use more.
'tabix' executable not found in $PATH. tabix() will use htslib to make queries instead which can be slower. See ?tabix for details.
> 
> test_check("iscream")
iscream now using 1 of 2 available threads.
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iscream now using 1 of 2 available threads.
iscream now using 2 of 2 available threads.
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 353 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• tabix_installed is not TRUE (2): 'test-tabix.R:59:3', 'test-tabix.R:120:3'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 353 ]
> 
> proc.time()
   user  system elapsed 
  4.452   0.290   4.769

Example timings

iscream.Rcheck/iscream-Ex.timings

nameusersystemelapsed
get_df_string0.0060.0010.006
get_granges_string0.8580.0290.886
get_threads0.0000.0000.001
htslib_version000
make_mat0.0150.0030.021
make_mat_bsseq3.3830.0993.510
query_chroms0.0000.0000.001
set_log_level0.0010.0000.001
set_threads0.0010.0000.001
summarize_meth_regions0.0090.0030.011
summarize_regions0.0190.0030.024
tabix0.0900.0100.101
validate_log_level0.0010.0000.000