* using log directory ‘/srv/hornik/tmp/CRAN_pretest/primeDB.Rcheck’ * using R Under development (unstable) (2025-07-18 r88431) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘primeDB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘primeDB’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Zhizhuo Zhang ’ New submission License components with restrictions and base license permitting such: MIT + file LICENSE File 'LICENSE': MIT License Copyright (c) 2025 Zhizhuo Zhang Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Possibly misspelled words in DESCRIPTION: Greengenes (10:47) RESTful (7:96) microbiome (7:68) * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘primeDB’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘api-v1.md’ ‘examples’ ‘test.R’ ‘test_all_functions.R’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... 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 ... [3s/3s] NOTE get_abundance_cache: no visible global function definition for ‘read.csv’ get_abundance_sample: no visible global function definition for ‘read.csv’ plot_distributions: no visible global function definition for ‘head’ plot_distributions: no visible binding for global variable ‘ymax’ plot_distributions: no visible binding for global variable ‘ymin’ plot_distributions: no visible binding for global variable ‘category’ plot_distributions: no visible binding for global variable ‘labelPosition’ plot_distributions: no visible binding for global variable ‘label’ Undefined global functions or variables: category head label labelPosition read.csv ymax ymin Consider adding importFrom("utils", "head", "read.csv") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/8s] ERROR Running examples in ‘primeDB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_sample_metadata > ### Title: Get Sample Metadata > ### Aliases: get_sample_metadata > > ### ** Examples > > metadata <- get_sample_metadata(c("DRR396974", "DRR396975")) Processing 2 samples in single batch... Completed processing 2 samples. > print(metadata) Run AvgSpotLen Bases BioProject BioSample Collection_Date 1 DRR396974 600 18183021 PRJDB13875 SAMD00518188 2020-08-18 2 DRR396975 600 13995744 PRJDB13875 SAMD00518189 2020-09-01 Experiment Country Continent Instrument Library_Name Release_Date 1 DRX382753 Japan Asia Illumina MiSeq NA 2024-01-03T00:00:00Z 2 DRX382754 Japan Asia Illumina MiSeq NA 2024-01-03T00:00:00Z Create_Date Sample_Name SRA_Study Project_name Time_series 1 2024-01-03T22:02:00Z F-NCNP005 DRP010964 MUSC-JP-2024 no 2 2024-01-03T22:02:00Z F-NCNP008 DRP010964 MUSC-JP-2024 no Comparison Matched Systems Body_Site Phenotype Doi 1 yes no Digestive System/Gut Stool/feces Healthy NA 2 yes no Digestive System/Gut Stool/feces Healthy NA Library_Layout Primer_Cut Primer_Par Denoise_Par Collapse 1 Paired Yes -p -b -d -p -F 250 -R 140 Silva and greengenes2 2 Paired Yes -p -b -d -p -F 250 -R 140 Silva and greengenes2 Sequencing_Quality Filter_Pass Variable_Region Sequencing_Type Note 1 Good Excellent V1-V2 2×300 NA 2 Good Excellent V1-V2 2×300 NA Time_Point Study_Group Participant_Id Host_Age Host_Sex Host_Height 1 NA Control NCNP005 NA NA NA 2 NA Control NCNP008 NA NA NA Host_Weight Host_BMI Host_Menopausal_Status Race_or_Ethnicity Host_Birth_Year 1 NA NA NA NA NA 2 NA NA NA NA NA Host_Country_Birth Smoke_Status Drinking_Status Diet_Type Probiotic_Frequency 1 NA NA NA NA NA 2 NA NA NA NA NA Teethbrushing_Frequency Sleep_Duration Tumor_Stage Node_Stage Metastasis 1 NA NA NA NA NA 2 NA NA NA NA NA Antibiotic_Route Antibiotics_Use Monobutyl_Phthalate_Presence 1 NA NA NA 2 NA NA NA Monoethyl_Phthalate_Presence Vaginal_pH Antibiotic_Status Anti_Fungal 1 NA NA NA NA 2 NA NA NA NA ALL_Type Endo_C_Value Endo_M_Value On_PPI Neoadjuvant Adjuvant Pepsin_D 1 NA NA NA NA NA NA NA 2 NA NA NA NA NA NA NA Pepsin_Level RSI_D RSI_Score Ihmc_medication_code Post_Pre_Surgery 1 NA NA NA NA NA 2 NA NA NA NA NA Abnormal_Uterine_Bleeding Confirmed_Adenomyosis Confirmed_Cysts 1 NA NA NA 2 NA NA NA Confirmed_Fibroids Endo_Location Endo_Stage Heavy_Menstrual_Bleeding 1 NA NA NA NA 2 NA NA NA NA Irregular_Menstrual_Bleeding Sperm_Concentration Sperm_Motility Fertility 1 NA NA NA NA 2 NA NA NA NA Dominant_Hand 1 NA 2 NA > > # For large datasets, batch processing is automatic > large_metadata <- get_sample_metadata(large_run_list) Error: object 'large_run_list' not found Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [0s/0s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [6s/56s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 NOTEs