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Merged
davidliwei merged 3 commits into from
Jul 9, 2026
Merged

Compiled-code stdout fix + set Wei Li as maintainer (Bioc) #12

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20eefef
Route compiled-code output to the R console (Bioconductor)
davidliwei Jul 9, 2026
8d5365b
Set Wei Li as package maintainer
davidliwei Jul 9, 2026
695e421
Address Copilot review: harden C++ file I/O and remove stdin read
davidliwei Jul 9, 2026
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -4,8 +4,8 @@ Title: Identify genes associated with multiple expression phenotypes in single-c
Version: 0.99.0
Date: 2026-07-09
Authors@R: c(
person("Wei", "Li", role = "aut"),
person("Xiaolong", "Cheng", email = "xiaolongcheng1120@gmail.com", role = c("aut", "cre")),
person("Wei", "Li", email = "li.david.wei@gmail.com", role = c("aut", "cre")),
person("Xiaolong", "Cheng", email = "xiaolongcheng1120@gmail.com", role = "aut"),
person("Lin", "Yang", role = "aut"))
Description: scMAGeCK is a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data (CROP-seq).
License: BSD_2_clause + file LICENSE
Expand Down
3 changes: 3 additions & 0 deletions NEWS.md
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Expand Up @@ -8,4 +8,7 @@
`FetchData()` with `layer=` (defunct in SeuratObject >= 5.4).
- The bundled example object is now stored in the Seurat v5 format.
* `DESCRIPTION` now requires `Seurat (>= 5.0.0)`.
* Compiled code (RRA) now writes diagnostics to the R console via
`Rcpp::Rcout`/`Rcpp::Rcerr`/`Rprintf` instead of `std::cout`/`printf`.
* R CMD check / BiocCheck clean-up (dead code, namespace, docs, examples).
* Version reset to 0.99.0 for Bioconductor resubmission.
97 changes: 49 additions & 48 deletions src/RRA.cpp
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Expand Up @@ -20,6 +20,7 @@
#include <map>
#include <iostream>
#include <fstream>
#include <Rcpp.h>
#include <algorithm>

using namespace std;
Expand Down Expand Up @@ -100,7 +101,7 @@ int loadControlSeq(const char* fname){
ifstream fh;
fh.open(fname);
if(!fh.is_open()){
cerr<<"Error opening "<<fname<<endl;
Rcpp::Rcerr<<"Error opening "<<fname<<endl;
}
Comment on lines 101 to 106
string oneline;
int ncount=0;
Expand All @@ -113,15 +114,15 @@ int loadControlSeq(const char* fname){
}
//oneline.erase( remove(oneline.begin(), oneline.end(), '\r'), oneline.end() );
//oneline.erase( remove(oneline.begin(), oneline.end(), '\n'), oneline.end() );
//cout<<oneline<<"#"<<oneline.size()<<endl;
//Rcpp::Rcout<<oneline<<"#"<<oneline.size()<<endl;
ControlSeqMap[oneline]=ncount;

ncount++;
}
fh.close();
ControlSeqPercentile = new double[ncount];
for(int i=0;i<ncount;i++) ControlSeqPercentile[i]=-1.0;
cout<<ControlSeqMap.size()<<" control sequences loaded.\n";
Rcpp::Rcout<<ControlSeqMap.size()<<" control sequences loaded.\n";
return 0;
}

Expand All @@ -147,7 +148,7 @@ int RRA_main (vector<string> & argv) {
return 0;
}

printf("Welcome to RRA v %s.\n", RRA_VERSION);
Rprintf("Welcome to RRA v %s.\n", RRA_VERSION);
inputFileName[0] = 0;
outputFileName[0] = 0;
maxPercentile = 0.1;
Expand Down Expand Up @@ -182,7 +183,7 @@ int RRA_main (vector<string> & argv) {
}
if (argv[i-1] == "--skip-gene"){
string sn(argv[i]);
cout<<"Skipping gene "<<sn<<" for permutation ..."<<endl;
Rcpp::Rcout<<"Skipping gene "<<sn<<" for permutation ..."<<endl;
gene_to_skip[sn]=0;
}
if (argv[i-1] == "--min-percentage-goodsgrna"){
Expand All @@ -204,19 +205,19 @@ int RRA_main (vector<string> & argv) {

if ((inputFileName[0]==0)||(outputFileName[0]==0))
{
cerr<<"Error: input file or output file name not set.\n";
Rcpp::Rcerr<<"Error: input file or output file name not set.\n";
PrintCommandUsage(argv[0].c_str());
return -1;
}

if ((maxPercentile>1.0)||(maxPercentile<0.0))
{
cerr<<("Error: maxPercentile should be within 0.0 and 1.0\n");
Rcpp::Rcerr<<("Error: maxPercentile should be within 0.0 and 1.0\n");
return -1;
}
if ((minPercentile>1.0))
{
cerr<<("Error: minPercentile should be less than 1.0\n");
Rcpp::Rcerr<<("Error: minPercentile should be less than 1.0\n");
return -1;
}

Expand All @@ -225,28 +226,28 @@ int RRA_main (vector<string> & argv) {
assert(groups!=NULL);
assert(lists!=NULL);

printf("Reading input file...\n");
Rprintf("Reading input file...\n");

flag = ReadFile(inputFileName, groups, MAX_GROUP_NUM, &groupNum, lists, MAX_LIST_NUM, &listNum);

if (flag<=0){
cerr<<"\nError: reading ranking file ...\n";
Rcpp::Rcerr<<"\nError: reading ranking file ...\n";
return -1;
}

cerr<<("Computing lo-values for each group...\n");
Rcpp::Rcerr<<("Computing lo-values for each group...\n");

if (ProcessGroups(groups, groupNum, lists, listNum, minPercentile, maxPercentile)<=0)
{
cerr<<("\nError: processing groups failed.\n");
Rcpp::Rcerr<<("\nError: processing groups failed.\n");
return -1;
}

cerr<<("Computing false discovery rate...\n");
Rcpp::Rcerr<<("Computing false discovery rate...\n");

if(rand_passnum*groupNum<100000 && has_specified_rand_passnum_parameter==false){
rand_passnum=100000/groupNum+1;
cout<<"Increase the number of permutations to "<<rand_passnum<<" to get precise p values. To avoid this, use the --permutation option.\n";
Rcpp::Rcout<<"Increase the number of permutations to "<<rand_passnum<<" to get precise p values. To avoid this, use the --permutation option.\n";
}

if(permutation_by_group){
Expand All @@ -256,37 +257,37 @@ int RRA_main (vector<string> & argv) {
}
if (i<=0)
{
cerr<<("\nError: computing FDR failed.\n");
Rcpp::Rcerr<<("\nError: computing FDR failed.\n");
return -1;
}
adjustFDR(groups,groupNum);

cerr<<("Saving to output file...\n");
Rcpp::Rcerr<<("Saving to output file...\n");

if (SaveGroupInfo(outputFileName, groups, groupNum)<=0)
{
cerr<<("\nError: saving output file failed.\n");
Rcpp::Rcerr<<("\nError: saving output file failed.\n");
return -1;
}

cerr<<("RRA completed.\n");
Rcpp::Rcerr<<("RRA completed.\n");

for(i=0;i<groupNum;i++)
delete[] groups[i].items;
free(groups);

cerr<<("Groups deletion complete.\n");
Rcpp::Rcerr<<("Groups deletion complete.\n");

for (i=0;i<listNum;i++)
{
delete[] lists[i].values;
}
free(lists);

cerr<<("Lists deletion complete.\n");
Rcpp::Rcerr<<("Lists deletion complete.\n");

if(UseControlSeq){
cerr<<("ControlSeqPercentile deletion complete.\n");
Rcpp::Rcerr<<("ControlSeqPercentile deletion complete.\n");
delete[] ControlSeqPercentile;
}

Expand All @@ -298,21 +299,21 @@ int RRA_main (vector<string> & argv) {
void PrintCommandUsage(const char *command)
{
//print the options of the command
printf("%s - Robust Rank Aggreation v %s.\n", command, RRA_VERSION);
printf("usage:\n");
printf("-i <input data file>. Format: <item id> <group id> <list id> <value> [<probability>] [<chosen>]\n");
printf("-o <output file>. Format: <group id> <number of items in the group> <lo-value> <false discovery rate>\n");
printf("-p <maximum percentile>. RRA only consider the items with percentile smaller than this parameter. Default=0.1\n");
printf("-P <minimum percentile>. RRA only consider the items with percentile greater than this parameter. Default=-1.0\n");
printf("--control <control_sgrna list>. A list of control sgRNA names.\n");
printf("--permutation <int>. The number of rounds of permutation. Increase this value if the number of genes is small. Default 100.\n");
printf("--no-permutation-by-group. By default, gene permutation is performed separately, by their number of sgRNAs. Turning this option will perform permutation on all genes together. This makes the program faster, but the p value estimation is accurate only if the number of sgRNAs per gene is approximately the same.\n");
printf("--skip-gene <gene_name>. Genes to skip from doing permutation. Specify it multiple times if you need to skip more than 1 genes.\n");
printf("--min-percentage-goodsgrna <min percentage>. Filter genes that have too few percentage of 'good sgrnas', or sgrnas that fall below the -p threshold. Must be a number between 0-1. Default 0 (do not filter genes).\n");
printf("--min-number-goodsgrna <min number>. Filter genes that have too few number of 'good sgrnas', or sgrnas that fall below the -p threshold. Must be an integer. Default 0 (do not filter genes). \n");
printf("--max-sgrnapergene-permutation <max number>. Only permute genes by group if the number of sgRNAs per gene is smaller than this number. This will save a lot of time if some regions are targeted by a large number of sgRNAs (usually hundreds). Must be an integer. Default 100. \n");
printf("example:\n");
printf("%s -i input.txt -o output.txt -p 0.1 \n", command);
Rprintf("%s - Robust Rank Aggreation v %s.\n", command, RRA_VERSION);
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Rprintf("usage:\n");
Rprintf("-i <input data file>. Format: <item id> <group id> <list id> <value> [<probability>] [<chosen>]\n");
Rprintf("-o <output file>. Format: <group id> <number of items in the group> <lo-value> <false discovery rate>\n");
Rprintf("-p <maximum percentile>. RRA only consider the items with percentile smaller than this parameter. Default=0.1\n");
Rprintf("-P <minimum percentile>. RRA only consider the items with percentile greater than this parameter. Default=-1.0\n");
Rprintf("--control <control_sgrna list>. A list of control sgRNA names.\n");
Rprintf("--permutation <int>. The number of rounds of permutation. Increase this value if the number of genes is small. Default 100.\n");
Rprintf("--no-permutation-by-group. By default, gene permutation is performed separately, by their number of sgRNAs. Turning this option will perform permutation on all genes together. This makes the program faster, but the p value estimation is accurate only if the number of sgRNAs per gene is approximately the same.\n");
Rprintf("--skip-gene <gene_name>. Genes to skip from doing permutation. Specify it multiple times if you need to skip more than 1 genes.\n");
Rprintf("--min-percentage-goodsgrna <min percentage>. Filter genes that have too few percentage of 'good sgrnas', or sgrnas that fall below the -p threshold. Must be a number between 0-1. Default 0 (do not filter genes).\n");
Rprintf("--min-number-goodsgrna <min number>. Filter genes that have too few number of 'good sgrnas', or sgrnas that fall below the -p threshold. Must be an integer. Default 0 (do not filter genes). \n");
Rprintf("--max-sgrnapergene-permutation <max number>. Only permute genes by group if the number of sgRNAs per gene is smaller than this number. This will save a lot of time if some regions are targeted by a large number of sgRNAs (usually hundreds). Must be an integer. Default 100. \n");
Rprintf("example:\n");
Rprintf("%s -i input.txt -o output.txt -p 0.1 \n", command);

}

Expand Down Expand Up @@ -381,7 +382,7 @@ int ProcessGroups(GROUP_STRUCT *groups, int groupNum, LIST_STRUCT *lists, int li
if(validsgs<=1){
isallone=true;
}
//printf("Gene: %s\n",groups[i].name);
//Rprintf("Gene: %s\n",groups[i].name);
if(isallone){
ComputeLoValue(tmpF, validsgs, groups[i].loValue, minPercentile,maxPercentile, groups[i].goodsgrnas);
}else{
Expand All @@ -392,7 +393,7 @@ int ProcessGroups(GROUP_STRUCT *groups, int groupNum, LIST_STRUCT *lists, int li
if(groups[i].controlsgs==groups[i].itemNum){
string sn(groups[i].name);
gene_to_skip[sn]=1;
cout<<"Skipping gene "<<sn<<" for permutation ..."<<endl;
Rcpp::Rcout<<"Skipping gene "<<sn<<" for permutation ..."<<endl;
}
}
}//end i loop
Expand All @@ -403,7 +404,7 @@ int ProcessGroups(GROUP_STRUCT *groups, int groupNum, LIST_STRUCT *lists, int li
if(UseControlSeq){
for(map<string,int>::iterator mit = ControlSeqMap.begin(); mit != ControlSeqMap.end(); mit++){
if(ControlSeqPercentile[mit->second]<0){
cerr<<"Warning: sgRNA "<<mit->first<<" not found in the ranked list. \n";
Rcpp::Rcerr<<"Warning: sgRNA "<<mit->first<<" not found in the ranked list. \n";
//ControlSeqPercentile[mit->second]=0.5;
}
}
Expand Down Expand Up @@ -526,12 +527,12 @@ int ComputeLoValue_Prob(double *percentiles, //array of percentiles
}


if(PRINT_DEBUG) printf("probs:");
if(PRINT_DEBUG) Rprintf("probs:");
for(i=0;i<num;i++)
{
if(PRINT_DEBUG) printf("%f,",probValue[i]);
if(PRINT_DEBUG) Rprintf("%f,",probValue[i]);
}
if(PRINT_DEBUG) printf("\n");
if(PRINT_DEBUG) Rprintf("\n");

accuLoValue=0.0;
for (pid=1;pid<(1<<num);pid++)
Expand Down Expand Up @@ -571,10 +572,10 @@ int ComputeLoValue_Prob(double *percentiles, //array of percentiles
}
real_i = real_i + 1;
}
if(PRINT_DEBUG) printf("pid: %d, prob:%e, score: %f\n",pid,c_prob,tmpLoValue);
if(PRINT_DEBUG) Rprintf("pid: %d, prob:%e, score: %f\n",pid,c_prob,tmpLoValue);
accuLoValue=accuLoValue+tmpLoValue*c_prob;
}
if(PRINT_DEBUG) printf("total: %f\n",accuLoValue);
if(PRINT_DEBUG) Rprintf("total: %f\n",accuLoValue);

loValue = accuLoValue;

Expand All @@ -596,7 +597,7 @@ int adjustFDR(GROUP_STRUCT *groups, int groupNum){
ngn++;
}
}
cout<<"Number of genes under FDR adjustment: "<<ngn<<endl;
Rcpp::Rcout<<"Number of genes under FDR adjustment: "<<ngn<<endl;
vector<double> pvalue_in;
for(i=0;i<groupNum;i++){
if(groups[i].isbad==0){
Expand Down Expand Up @@ -689,14 +690,14 @@ int ComputePermutationbyNumSG(GROUP_STRUCT *groups, int groupNum, double minPerc
n_control++;
}
}
cout<<"Total # control sgRNAs: "<<n_control<<endl;
Rcpp::Rcout<<"Total # control sgRNAs: "<<n_control<<endl;
}

for(map<int,int>::iterator mii=itemNumMap.begin();mii!=itemNumMap.end();mii++){
int sgrnanum=mii->first;
if(sgrnanum<=max_sgnum_permutation_by_group){// to avoid permutations on genes with too many sgRNAs (take too much time)
randLoValueNum = 0;
cout<<"Permuting genes with "<<sgrnanum<<" sgRNAs..."<<endl;
Rcpp::Rcout<<"Permuting genes with "<<sgrnanum<<" sgRNAs..."<<endl;
for (i=0;i<scanPass;i++){
for (j=0;j<groupNum;j++){
int validsgs=0;
Expand Down Expand Up @@ -844,7 +845,7 @@ int ComputePermutation(GROUP_STRUCT *groups, int groupNum, double minPercentile,
n_control++;
}
}
cout<<"Total # control sgRNAs: "<<n_control<<endl;
Rcpp::Rcout<<"Total # control sgRNAs: "<<n_control<<endl;
}

for (i=0;i<scanPass;i++){
Expand Down
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