Validation Report - ftrCOOL@2.0.0
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package ftrCOOL
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 166 |
| has_vignettes | 0 |
| export_help | 166 |
| has_website | FALSE |
| has_maintainer | Sare Amerifar sare.ameri.01@gmail.com |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| assess_size_codebase | 14796 |
| has_bug_reports_url | 0 |
| downloads_1yr | 3467 |
| reverse_dependencies | 3 |
| has_examples | 1 |
| dependencies | 2 |
| license | GPL-3 |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | stats | Imports |
| 2 | utils | Imports |
Package dependencies
Reverse dependencies
Overall the package has 3 reverse dependencies:
EpiSemble, GB5mcPred, OpEnHiMR
Namespace
Overall the package has 166 exported objects. 166 are documented:
AA2Binary AAindex AAKpartComposition
TRUE TRUE TRUE
AAutoCor AESNN3 alphabetCheck
TRUE TRUE TRUE
ANF_DNA ANF_RNA APAAC
TRUE TRUE TRUE
APkNUCdi_DNA APkNUCdi_RNA APkNUCTri_DNA
TRUE TRUE TRUE
ASA ASDC ASDC_DNA
TRUE TRUE TRUE
ASDC_RNA AutoCorDiNUC_DNA AutoCorDiNUC_RNA
TRUE TRUE TRUE
AutoCorTriNUC_DNA binary_3bit_T1 binary_3bit_T2
TRUE TRUE TRUE
binary_3bit_T3 binary_3bit_T4 binary_3bit_T5
TRUE TRUE TRUE
binary_3bit_T6 binary_3bit_T7 binary_5bit_T1
TRUE TRUE TRUE
binary_5bit_T2 binary_6bit BLOSUM62
TRUE TRUE TRUE
CkSAApair CkSGAApair CkSNUCpair_DNA
TRUE TRUE TRUE
CkSNUCpair_RNA codonAdaptionIndex CodonFraction
TRUE TRUE TRUE
CodonUsage_DNA CodonUsage_RNA conjointTriad
TRUE TRUE TRUE
conjointTriadKS CTD CTDC
TRUE TRUE TRUE
CTDD CTDT DDE
TRUE TRUE TRUE
DiNUC2Binary_DNA DiNUC2Binary_RNA DiNUCindex_DNA
TRUE TRUE TRUE
DiNUCindex_RNA DisorderB DisorderC
TRUE TRUE TRUE
DisorderS DistancePair DPCP_DNA
TRUE TRUE TRUE
DPCP_RNA EAAComposition EffectiveNumberCodon
TRUE TRUE TRUE
EGAAComposition EIIP ENUComposition_DNA
TRUE TRUE TRUE
ENUComposition_RNA ExpectedValKmerNUC_DNA ExpectedValKmerNUC_RNA
TRUE TRUE TRUE
ExpectedValueAA ExpectedValueGAA ExpectedValueGKmerAA
TRUE TRUE TRUE
ExpectedValueKmerAA fa.read fickettScore
TRUE TRUE TRUE
G_Ccontent_DNA G_Ccontent_RNA GAAKpartComposition
TRUE TRUE TRUE
GrpDDE kAAComposition kGAAComposition
TRUE TRUE TRUE
KNN_DNA KNN_RNA KNNPeptide
TRUE TRUE TRUE
KNNProtein kNUComposition_DNA kNUComposition_RNA
TRUE TRUE TRUE
LocalPoSpKAAF LocalPoSpKNUCF_DNA LocalPoSpKNUCF_RNA
TRUE TRUE TRUE
maxORF maxORF_RNA maxORFlength_DNA
TRUE TRUE TRUE
maxORFlength_RNA Mismatch_DNA Mismatch_RNA
TRUE TRUE TRUE
MMI_DNA MMI_RNA nameKmer
TRUE TRUE TRUE
NCP_DNA NCP_RNA needleman
TRUE TRUE TRUE
nonStandardSeq NUC2Binary_DNA NUC2Binary_RNA
TRUE TRUE TRUE
NUCKpartComposition_DNA NUCKpartComposition_RNA OPF_10bit
TRUE TRUE TRUE
OPF_7bit_T1 OPF_7bit_T2 OPF_7bit_T3
TRUE TRUE TRUE
PCPseDNC PS2_DNA PS2_RNA
TRUE TRUE TRUE
PS3_DNA PS3_RNA PS4_DNA
TRUE TRUE TRUE
PS4_RNA PSEAAC PseEIIP
TRUE TRUE TRUE
PSEkNUCdi_DNA PSEkNUCdi_RNA PSEkNUCTri_DNA
TRUE TRUE TRUE
PseKRAAC_T1 PseKRAAC_T10 PseKRAAC_T11
TRUE TRUE TRUE
PseKRAAC_T12 PseKRAAC_T13 PseKRAAC_T14
TRUE TRUE TRUE
PseKRAAC_T15 PseKRAAC_T16 PseKRAAC_T2
TRUE TRUE TRUE
PseKRAAC_T3A PseKRAAC_T3B PseKRAAC_T4
TRUE TRUE TRUE
PseKRAAC_T5 PseKRAAC_T6A PseKRAAC_T6B
TRUE TRUE TRUE
PseKRAAC_T7 PseKRAAC_T8 PseKRAAC_T9
TRUE TRUE TRUE
PSSM PSTNPds PSTNPss_DNA
TRUE TRUE TRUE
PSTNPss_RNA QSOrder readASAdir
TRUE TRUE TRUE
readDisDir readPSSMdir readss2Dir
TRUE TRUE TRUE
readTorsionDir revComp SAAC
TRUE TRUE TRUE
SGAAC SOCNumber SSEB
TRUE TRUE TRUE
SSEC SSES TorsionAngle
TRUE TRUE TRUE
TPCP_DNA TriNUCindex_DNA Zcurve12bit_DNA
TRUE TRUE TRUE
Zcurve12bit_RNA Zcurve144bit_DNA Zcurve144bit_RNA
TRUE TRUE TRUE
Zcurve36bit_DNA Zcurve36bit_RNA Zcurve48bit_DNA
TRUE TRUE TRUE
Zcurve48bit_RNA Zcurve9bit_DNA Zcurve9bit_RNA
TRUE TRUE TRUE
zSCALE
TRUE Examples
There are 166 help pages with examples, from 166 (100.00 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.2 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-03-17 03:33:03 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.3 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.50 jsonlite_1.9.1
[10] xfun_0.51 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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GITHUB_TRIGGERING_ACTOR
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RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
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PHARMAPKGS_REMOTE_REPO
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PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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YES
PWD /home/runner/work/pharmapkgs/pharmapkgs
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QUARTO_PROFILE
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R_SHARE_DIR /opt/R/4.4.3/lib/R/share
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RUNNER_ENVIRONMENT github-hosted
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
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$bitmapType
[1] "cairo"
$browser
[1] "xdg-open"
$browserNLdisabled
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$callr.condition_handler_cli_message
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else {
cli_server_default(msg)
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}
<bytecode: 0x558c022a0330>
<environment: namespace:cli>
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<environment: namespace:knitr>
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$rlang_trace_top_env
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$scipen
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$show.coef.Pvalues
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$show.signif.stars
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$showErrorCalls
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$str
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$str$vec.len
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$str$list.len
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$str$deparse.lines
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$str$formatNum
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<environment: 0x558c0177b688>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
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mode "w+b"
text "binary"
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can read "yes"
can write "yes"
$ts.eps
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$unzip
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$width
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